Index (Anchor - merged Javadoc across key repositories (documentation work in progress). 0.0.1-SNAPSHOT API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes All Packages

A

absolute() - Method in class org.anchoranalysis.spatial.point.Tuple3d
AbsoluteValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
AbsoluteValue() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
accept(int) - Method in interface org.anchoranalysis.core.functional.checked.CheckedIntConsumer
accept(int, int) - Method in interface org.anchoranalysis.math.histogram.Histogram.BinConsumer
accept(int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.ScalarTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(int, int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.OffsettedScalarTwoDimensionalConsumer: Accepts a point
accept(int, int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.ScalarThreeDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
accept(ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.UpdatableBeforeCondition
accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.BeforeCondition
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.DistanceCondition
accept(ObjectMask, ObjectMask, ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.AfterCondition
accept(ObjectMask, ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
accept(ParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
accept(ParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.CheckParsedFilePathBag
accept(Point2i) - Method in interface org.anchoranalysis.spatial.point.consumer.PointTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(Point2i, int) - Method in interface org.anchoranalysis.spatial.point.consumer.OffsettedPointTwoDimensionalConsumer: Accepts a point like with a Consumer in general.
accept(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedConsumer
accept(S, T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedBiConsumer: Calls the function
accepted() - Method in interface org.anchoranalysis.annotation.mark.DualMarks: The accepted marks.
acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in interface org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationConditon
acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationList
acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfAllHigh
acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfLowDisconnected
AcceptIterationConditon - Interface in org.anchoranalysis.image.voxel.object.morphological.accept: A condition that must be fulfilled for a particular iteration of a morphological operation to be accepted.
AcceptIterationList - Class in org.anchoranalysis.image.voxel.object.morphological.accept
AcceptIterationList() - Constructor for class org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationList
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.BinaryKernel
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3: This method is deliberately not broken into smaller pieces to avoid inlining.
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3: This method is deliberately not broken into smaller pieces to avoid inlining.
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3ZOnly
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.ErosionKernel3: This method is deliberately not broken into smaller pieces to avoid inlining.
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3: This method is deliberately not broken into smaller pieces to avoid inlining.
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3NeighborMatchValue: This method is deliberately not broken into smaller pieces to avoid inlining.
acceptProposal(ToDoubleFunction<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
accepts(Class<?>) - Method in interface org.anchoranalysis.bean.initializable.property.PropertyDefiner
accepts(Class<?>) - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
acceptsAsSource(Class<?>) - Method in class org.anchoranalysis.bean.initializable.property.ExtractFromParam: Are the source-parameters acceptable for extraction? *
AccessObjectMask<T> - Interface in org.anchoranalysis.image.core.object.scale: Provides functions to provide access and creation to/from the object-mask representation of a generic type.
AccptProbCalculator<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization
AccptProbCalculator(AnnealScheme, ExtractScoreSize<T>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.AccptProbCalculator
activateDebugMode(String) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments: Activates debug-mode
add(double) - Method in class org.anchoranalysis.feature.energy.EnergyTotal
add(double) - Method in class org.anchoranalysis.plot.AxisLimits
add(double) - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
add(double, double, double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
add(int, int, int) - Method in class org.anchoranalysis.spatial.box.PointRange
add(int, long) - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
add(int, String) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
add(int, RGBColor) - Method in class org.anchoranalysis.core.color.ColorList
add(int, UpdatableMarkSet) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
add(Color) - Method in class org.anchoranalysis.core.color.ColorList
add(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.task.InputTypesExpected
add(Double) - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
add(Exception) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
add(Exception) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
add(Exception) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
add(String) - Method in interface org.anchoranalysis.bean.StringBeanCollection
add(String) - Method in class org.anchoranalysis.bean.StringList
add(String) - Method in class org.anchoranalysis.bean.StringSet
add(String) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Adds a feature-name
add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
add(String, boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Adds a new output-name to the set of recorded names.
add(String, int) - Method in class org.anchoranalysis.feature.name.FeatureNameMapToIndex: Adds a new featureName and index
add(String, int) - Method in class org.anchoranalysis.overlay.OverlayProperties
add(String, String) - Method in class org.anchoranalysis.overlay.OverlayProperties
add(String, StoreSupplier<Stack>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
add(String, StoreSupplier<TimeSequence>) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
add(String, StoreSupplier<TimeSequence>) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
add(String, StoreSupplier<T>) - Method in interface org.anchoranalysis.core.identifier.provider.store.NamedProviderStore
add(String, StoreSupplier<T>) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap: Adds an entry to the map
add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
add(String, Feature<T>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore: Adds a named-feature to the store.
add(String, Stack) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
add(String, Stack) - Method in class org.anchoranalysis.image.core.stack.NamedStacksUniformSize
add(String, Generator<T>) - Method in class org.anchoranalysis.io.generator.combined.CombinedListGenerator
add(String, EnergyScheme) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
add(String, Mark) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
add(String, Mark) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
add(String, Mark) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
add(String, S, NamedProviderStore<D>, CheckedFunction<S, D, OperationFailedException>) - Static method in class org.anchoranalysis.bean.store.BeanStoreAdder: Adds an item a container (using a bridge) and explicitly specifying a new name
add(String, T) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
add(Optional<String>, String, S) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName: Adds an item with an identifier
add(NamedBean<?>) - Method in class org.anchoranalysis.bean.define.Define: Adds a named-bean to our definitions, using the {#link GroupingRoot} annotation to determine a group where definitions are stored.
add(PermutationSetter) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterList
add(RGBColor) - Method in class org.anchoranalysis.core.color.ColorList
add(NameValue<T>) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
add(NamedProvider<T>) - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
add(NameValueSet<T>) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
add(StatefulMessageLogger) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
add(SubmittedJob) - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
add(Feature<? extends T>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
add(EnergyTotal) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
add(ResultsVector) - Method in class org.anchoranalysis.feature.results.ResultsVectorList
add(CacheTransferSource<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
add(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
add(Seed) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
add(Stack) - Method in class org.anchoranalysis.image.core.stack.TimeSequence
add(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
add(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannelsSimple
add(AcceptIterationConditon) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationList
add(ObjectMask) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
add(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
add(VoxelStatistics) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
add(VoxelsWrapper) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
add(MutableDirectory) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
add(FileType[]) - Method in class org.anchoranalysis.io.generator.ConcatenateFileTypes
add(OutputtedFile) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
add(OutputtedFile) - Method in class org.anchoranalysis.io.manifest.directory.Subdirectory
add(EnergySavedInd, VoxelizedMarkMemo, EnergyStackWithoutParams, EnergySchemeWithSharedFeatures) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
add(MemoCollection, VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
add(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
add(Mark, Color) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
add(Mark, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
add(UpdatableMarkSet) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
add(MemoForIndex) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
add(MemoForIndex, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
add(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
add(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
add(VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
add(CreateProposalVisualization) - Method in class org.anchoranalysis.mpp.proposer.visualization.CreateProposeVisualizationList
add(TerminationCondition) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
add(WeightedKernel<T>) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
add(AggregateReceiver<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
add(FeedbackReceiver<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
add(PeriodReceiver<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
add(IndexByRegion<T>) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
add(Overlay) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
add(Overlay, RGBColor) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
add(AnnotationGroup<T>) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
add(LevelResult) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
add(FileDetails) - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
add(BoundingBox) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
add(BoundingBox, T) - Method in class org.anchoranalysis.spatial.rtree.RTree: Adds a bounding-box with a corresponding index.
add(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d
add(Point2i) - Method in class org.anchoranalysis.spatial.point.Point2d
add(Point2i) - Method in class org.anchoranalysis.spatial.point.Point2i
add(Point3i) - Method in class org.anchoranalysis.spatial.box.PointRange
add(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3d
add(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i
add(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
add(S, T) - Method in interface org.anchoranalysis.plugin.image.task.grouped.AddToAggregateItem
add(T) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing: Outputs an additional element in the sequence.
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer: Adds a element to the summary.
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
add(T, String) - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
add(T, S) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed: Outputs an additional element in the sequence.
addAcceptedAnnotation(AssignmentOverlapFromPairs) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
addAcceptedAnnotation(T) - Method in interface org.anchoranalysis.plugin.annotation.comparison.AddAnnotation
addAcceptedAnnotation(T) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
addAcceptedAnnotation(T) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
addAdditionalOptions(Options) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
addAdditionalOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions
addAll(int, Collection<? extends UpdatableMarkSet>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
addAll(Collection<? extends ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
addAll(Collection<? extends UpdatableMarkSet>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
addAll(Collection<AnnotationGroup<T>>) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
addAll(Define) - Method in class org.anchoranalysis.bean.define.Define: Adds all the named-beans (shallow copy) from source to th ecurrent map
addAll(ColorList) - Method in class org.anchoranalysis.core.color.ColorList
addAll(FeatureList<? extends T>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
addAll(ObjectCollection) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
addAll(ColoredMarks) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
addAll(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
addAll(MarkCollection, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
addAll(MemoForIndex) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
addAll(OverlayCollection) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
addAllOutputNamesTo(OutputEnabledMutable) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter: Adds all possible output-names to a OutputEnabledMutable.
addAllScaled(ColorList, double) - Method in class org.anchoranalysis.core.color.ColorList
addAllToUpdatablePairList(ListUpdatableMarkSetCollection) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
AddAnnotation<T extends Assignment> - Interface in org.anchoranalysis.plugin.annotation.comparison
addBasicOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions
addBean(String, Object) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
addBean(String, Object) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
addBean(String, Object) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
addBeansFromList(Define, List<NamedBean<?>>) - Static method in class org.anchoranalysis.bean.define.adder.DefineAdderUtilities
addBlankChannel() - Method in class org.anchoranalysis.image.core.stack.Stack
addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
addBoundChangeListener(BoundChangeListener) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncompleteDynamic
addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
addBuffer(FloatBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferFloat
addBuffer(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferByte
addBuffer(UnsignedIntBuffer, UnsignedIntBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferInt
addBuffer(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferShort
addBuffer(T, T) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer
addChangeID(Mark, Color) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
addChangeID(Mark, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
addChannel(Channel) - Method in class org.anchoranalysis.image.core.stack.Stack
addChannel(Channel) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
addChannelsFrom(Stack) - Method in class org.anchoranalysis.image.core.stack.Stack
AddConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
AddConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.AddConstant
AddConstantTo<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
AddConstantTo() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
AddCriteria<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria: Add Criteria
AddCriteriaDistanceTo - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
AddCriteriaDistanceTo() - Constructor for class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
AddCriteriaEnergyPair - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaEnergyPair(FeatureList<FeatureInputPairMemo>, AddCriteriaPair) - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
AddCriteriaFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
AddCriteriaFeatureRelationThreshold() - Constructor for class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
AddCriteriaNever<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaNever() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
AddCriteriaOr - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaOr() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
AddCriteriaPair - Class in org.anchoranalysis.mpp.feature.addcriteria
AddCriteriaPair() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
addCustomNames(FeatureList<?>) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Add the customNames of a feature
addCustomNamesWithPrefix(String, FeatureList<?>) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Add the customNames of a feature with a Prefix
AddDistanceTransform - Class in org.anchoranalysis.plugin.fiji.bean.define: Performs a Watershed on an EDT transform by bundling together several other beans
AddDistanceTransform() - Constructor for class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
addDoubleAsString(String, double) - Method in class org.anchoranalysis.overlay.OverlayProperties
AddDualTransformer - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
AddDualTransformer() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
addEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Add an edge between two vertices.
addEdge(V, V, P) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Add an edge between two vertices.
AddEdgeFilters - Class in org.anchoranalysis.plugin.imagej.bean.define
AddEdgeFilters() - Constructor for class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
addEdges(V, Collection<V>) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Adds edge(s) from the vertex from to each element in toCollection.
addEnabledOutputFirst(String...) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Adds enabled first-level outputs.
addEnabledOutputs(OutputEnabledMutable) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Adds enabled outputs from another OutputEnabledMutable.
addEnabledOutputSecond(String, String...) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Adds enabled second-level outputs.
AddEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
AddEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.AddEnergy
addErrorDescription(StringBuilder) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
addErrorDescription(StringBuilder) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
addErrorDescription(StringBuilder) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
addErrorLevel(String) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
addErrorLevel(String, AnchorBean<?>) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
addFeatureListToStore(FeatureList<T>, String, boolean, NamedFeatureStore<T>) - Static method in class org.anchoranalysis.feature.list.FeatureListStoreUtilities: Adds a feature-list to the store
addFeatureListToStoreNoDuplicateDirectly(NamedProvider<FeatureList<FeatureInput>>, SharedFeatureMulti) - Static method in class org.anchoranalysis.feature.list.FeatureListStoreUtilities
addField(Field) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
addFormatted(String, Object...) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
addFormatted(String, Object...) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
addFormatted(String, Object...) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
addForSlice(int, int) - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
addForSlice(int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
addFrom(List<NamedBean<?>>) - Method in class org.anchoranalysis.bean.BeanInstanceMap: Populates from a list of NamedBean.
addFrom(BeanInstanceMap) - Method in class org.anchoranalysis.bean.BeanInstanceMap: Populates the entries from another BeanInstanceMap
addFrom(NamedProvider<Stack>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
addFromWithPrefix(NamedProvider<Stack>, String) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
addFromXmlFile(Path) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap: Adds root-paths contained in a list of XML Beans in an xml file
addHistogram(Histogram) - Method in class org.anchoranalysis.math.histogram.Histogram
addIgnoreInfinity(double) - Method in class org.anchoranalysis.plot.AxisLimits
addIter(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
addIter(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
addIter(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
addLabelToDataset(DefaultCategoryDataset, T, int, String, String) - Method in class org.anchoranalysis.plot.index.BarPlot
addLabelToDataset(DefaultBoxAndWhiskerCategoryDataset, T, int, String, String) - Method in class org.anchoranalysis.plot.index.BoxPlot
addLabelToDataset(S, T, int, String, String) - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
addLeftObject(ObjectMask) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
addLeftObjects(ObjectCollection) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
addListOfBeansToCollection(String, HierarchicalConfiguration, Collection<T>, Object) - Static method in class org.anchoranalysis.bean.xml.factory.HelperListUtilities
addManifestExperimentFileSet(Collection<File>, ManifestDeserializer, Logger) - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
addMultiple(RGBColor, int) - Method in class org.anchoranalysis.core.color.ColorList
addNewPath(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels: Adds a new path with a point
addNoDuplicate(FeatureList<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
addObjectsNoBoundingBoxChange(Collection<T>) - Method in class org.anchoranalysis.spatial.box.BoundedList: Adds elements without changing the bounding-box
addObjectsToGraph(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
addObjectsWithColor(ObjectCollectionProvider, RGBColor) - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Adds objects from a ObjectCollectionProvider all with one specific color
addOperationRecorder(WriteOperationRecorder) - Method in class org.anchoranalysis.io.output.outputter.Outputter
addOperationRecorder(WriteOperationRecorder) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Adds an additional operation recorder alongside any existing recorders.
addPair(ObjectMask, ObjectMask, double) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
addPointsInMark(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
addPreserveName(List<NamedBean<S>>, NamedProviderStore<D>, CheckedFunction<S, D, OperationFailedException>) - Static method in class org.anchoranalysis.bean.store.BeanStoreAdder: Adds a list of named-items a container (using a bridge) using the same names in the destination container
addPreserveNameEmbedded(List<NamedBean<S>>, NamedProviderStore<D>, CheckedFunction<NamedBean<S>, D, OperationFailedException>) - Static method in class org.anchoranalysis.bean.store.BeanStoreAdder: Adds a list of named-items to a container (using a bridge) using the same names in the destination container
addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.Orientation
addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.Orientation
addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
addResultsFor(RowLabels, ResultsVector) - Method in class org.anchoranalysis.feature.io.results.group.GroupWriter: Adds a result to the group-writer, but doesn't write yet.
addResultsFor(RowLabels, ResultsVector) - Method in class org.anchoranalysis.feature.io.results.ResultsWriter: Adds feature-calculation results to be written.
addResultsFor(RowLabels, ResultsVectorWithThumbnail) - Method in interface org.anchoranalysis.plugin.image.task.feature.ExportFeatureResultsAdder: Adds labeled results (which makes a row in a feature-table, and possibly other outputs).
addResultsFor(RowLabels, ResultsVectorWithThumbnail) - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
addRightObject(ObjectMask) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
addRightObjects(ObjectCollection) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
addRow(List<TypedValue>) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Directly adds a row in the form of typed-values.
addRow(RowLabels, ResultsVector) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Directly adds a row of feature-values.
addShift(ReadableTuple3i) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath: Adds a shift to each point (modifying the existing points in memory), and returns them as a list
addSkippedAnnotationImage() - Method in interface org.anchoranalysis.plugin.annotation.comparison.AddAnnotation
addSkippedAnnotationImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
addSkippedAnnotationImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
addTo(Define) - Method in class org.anchoranalysis.bean.define.adder.Concatenate
addTo(Define) - Method in interface org.anchoranalysis.bean.define.adder.DefineAdder
addTo(Define) - Method in class org.anchoranalysis.bean.define.adder.FromXmlList
addTo(Define) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
addTo(Define) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
addTo(Define) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
addTo(ObjectMask, int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Adds a constant-value to each voxel but only for voxels inside an object-mask
addTo(S, T) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
AddToAggregateItem<S,T> - Interface in org.anchoranalysis.plugin.image.task.grouped: Adds an individual-item to an aggregate-item
AddToDefaults - Class in org.anchoranalysis.io.output.bean.rules: Adds additional outputs-names to be enabled to the defaults.
AddToDefaults() - Constructor for class org.anchoranalysis.io.output.bean.rules.AddToDefaults
addToErrorNode(ErrorNode) - Method in exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException
addToKeyValueParamsCollection(String, KeyValueParams) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
addToManager(MultiInputManager, String, String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManager
addToMarks(ColoredMarks) - Method in interface org.anchoranalysis.mpp.proposer.visualization.CreateProposalVisualization
addToMarks(ColoredMarks) - Method in class org.anchoranalysis.mpp.proposer.visualization.CreateProposeVisualizationList
addToRow(List<TypedValue>) - Method in class org.anchoranalysis.feature.io.csv.RowLabels: Adds the identifiers to a row to be outputted in a features CSV.
addToSharedObjects(MPPInitParams, ImageInitParams) - Method in interface org.anchoranalysis.mpp.io.input.InputForMPPBean
addToSharedObjects(MPPInitParams, ImageInitParams) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
addToSharedObjects(MPPInitParams, ImageInitParams) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
addToStackCollection(String, StackProvider) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
addToStackCollection(String, Stack) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
addToStore(NamedProviderStore<TimeSequence>) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
addToStore(NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
addToStore(NamedProviderStore<T>) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap: Copies all the existing entries into a NamedProvierStore
addToStore(NamedProviderStore<T>) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
addToTypeValueCollection(Collection<TypedValue>, int) - Method in class org.anchoranalysis.feature.results.ResultsVector
addToUpdatablePairList(ListUpdatableMarkSetCollection, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
addToVoxelList(int, int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
addUnannotatedImage() - Method in interface org.anchoranalysis.plugin.annotation.comparison.AddAnnotation
addUnannotatedImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
addUnannotatedImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
addUncoupledJobs(Collection<File>, ManifestDeserializer, Logger) - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition: Adds job-manifests that don't have corresponding experiment-manifests.
addUnused(Histogram) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactoryHistogramReuse
addUnused(Histogram) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitonFactoryHistogram
addUnused(T) - Method in interface org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactory
addVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Adds a vertex.
addVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Adds a vertex.
addVisitedPoint(Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels: Adds a visited-point to an existing path, or else makes a new one
addWeightedKernelFactories(List<WeightedKernel<T>>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
addWeightedKernelFactories(List<WeightedKernel<T>>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
addWeightedKernelFactories(List<WeightedKernel<T>>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
addWithIndex(RGBColor) - Method in class org.anchoranalysis.core.color.ColorList
addWithName(Define, String, AnchorBean<?>) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
addWithUnits(String, double, DoubleUnaryOperator, SpatialUnits.UnitSuffix) - Method in class org.anchoranalysis.overlay.OverlayProperties
AdjacentFile - Class in org.anchoranalysis.plugin.quick.bean.input
AdjacentFile() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile
adjacentVerticesOutgoing(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: The vertices that are connected to a particular vertex by an outgoing edge
adjacentVerticesOutgoing(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The vertices that are connected to a particular vertex by an outgoing edge
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
afterAllJobsAreExecuted(OutputSequenceIncrementing<Stack>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
afterAllJobsAreExecuted(ExperimentState, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
afterAllJobsAreExecuted(SharedState<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
afterAllJobsAreExecuted(SharedStateExportFeatures<S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
afterAllJobsAreExecuted(GroupedSharedState<S, T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
afterAllJobsAreExecuted(SharedStateSegmentInstance<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
afterAllJobsAreExecuted(SharedStateSelectedSlice, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
afterAllJobsAreExecuted(Summarizer<S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
afterAllJobsAreExecuted(FromCSVSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
afterAllJobsAreExecuted(S, InputOutputContext) - Method in class org.anchoranalysis.experiment.bean.task.Task: Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
afterAllJobsAreExecuted(S, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
AfterCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
afterCopying(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
afterCopying(Path, boolean) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming
afterCopying(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
afterCopying(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
aggEnd(Aggregator) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiver
aggEnd(Aggregator) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
AggIDCounter - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggIDCounter(int) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
AggregateAnnotations<S extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.aggregate: Aggregates many per-image annotations together in form of a CSV file.
AggregateAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
AggregateReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregateReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregateReceiverList() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MaxFeatureIntersectingObjects
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MinFeatureIntersectingObjectsAboveThreshold
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjectsAboveThreshold
AggregateTriggerBank<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregateTriggerBank(ExtractScoreSize<T>) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
Aggregator - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
Aggregator(int) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
AggregatorException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
AggregatorException() - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregatorException
AggregatorException(Exception) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregatorException
AggregatorException(String) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregatorException
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
aggReport(Reporting<T>, Aggregator) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiver
aggReport(Reporting<T>, Aggregator) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiver
aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
All - Class in org.anchoranalysis.io.output.bean.enabled: All outputs are allowed irrespective of outputName.
All - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects all possible channels from all possible stacks
All() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.All
ALL_DIMENSIONS - org.anchoranalysis.image.voxel.object.morphological.SelectDimensions: The dilation applies in all dimensions (X, Y and Z)
allChannelsHaveIdenticalType() - Method in class org.anchoranalysis.image.core.stack.Stack: Determines if all channels have an identical voxel data-type.
allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.core.stack.Stack: Determines if all channels have a specific data-type.
allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.core.stack.TimeSequence
allFileTypes() - Method in class org.anchoranalysis.io.generator.ConcatenateFileTypes
allHeaders() - Method in class org.anchoranalysis.feature.io.results.LabelHeaders: The non-group and group headers combined (in this order respectively)
allLabels(NoSharedState) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
allLabels(ImageCSVLabellerInitParams) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
allLabels(ImageLabellerStringMapInitParams<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
allLabels(T) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller: A set of identifiers for all groups that can be outputted by the labeller.
allMatchIntensity(ObjectMask, Voxels<T>, IntPredicate) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Do all points on an object-mask match a predicate on the point's voxel-intensity?
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Allocates a new buffer of unsigned-bytes.
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Allocates a new (direct) buffer of unsigned-ints.
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Allocates a new (direct) buffer of unsigned-shorts.
allocateBuffer() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
allocateFloat(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new float voxel-buffers of given size.
allocateFloatArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of float voxel-buffers of given size.
allocateUnsignedByte(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new unsigned byte voxel-buffer of given size.
allocateUnsignedByteArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of unsigned byte voxel-buffers of given size.
allocateUnsignedInt(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new unsigned int voxel-buffers of given size.
allocateUnsignedIntArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of unsigned int voxel-buffers of given size.
allocateUnsignedShort(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new unsigned short voxel-buffers of given size.
allocateUnsignedShortArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of unsigned short voxel-buffers of given size.
AllowEmpty - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a String is allowed be empty, otherwise by default it must be non-empty.
allSlices(Voxels, Function<U, T>, Function<AbstractNativeImg<S, T>, S>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.Wrap
AllSlicesMaskEverythingNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region: Only takes pixels where indexNonZero has a nonzero pixel
AllSlicesMaskEverythingNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
AllSlicesMaskNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region: Gets all slices where indexNonZero has at least one non-zero pixel in that slice
AllSlicesMaskNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
allSuccessful() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: Did all jobs execute and completely successfully?
AllValuesOff - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
AllValuesOff() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOff
AllValuesOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions: Creates a new mask of particular dimensionality where all values are ON
AllValuesOn() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOn
Always - Class in org.anchoranalysis.plugin.image.bean.object.match: Specifies a single object that will always be the "match" for whatever source object.
Always() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Always
ALWAYS_NEW - org.anchoranalysis.image.core.channel.convert.ConversionPolicy
AlwaysAllowed - Class in org.anchoranalysis.io.output.writer: Allows every output, irrespective of whether the OutputterChecked allows the output-name.
AlwaysAllowed(OutputterChecked, Optional<WriterExecuteBeforeEveryOperation>) - Constructor for class org.anchoranalysis.io.output.writer.AlwaysAllowed
alwaysExecuteBeforeCallingLibrary() - Static method in class org.anchoranalysis.plugin.opencv.CVInit: This routine must always be executed at least once before calling any routines in the OpenCV library
AlwaysNew<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.replace: Always create a new session-input with no reuse or caching
AlwaysNew(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.AlwaysNew: Constructor with default means of creating a session-input
AlwaysNew(CacheCreator, FindChildStrategy) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.AlwaysNew
AnchorBean<F> - Class in org.anchoranalysis.bean: The base class of all beans used in Anchor.
AnchorBean() - Constructor for class org.anchoranalysis.bean.AnchorBean
AnchorBeanFactory - Class in org.anchoranalysis.bean.xml.factory: Base class for all Anchor-specific bean factories
AnchorBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.AnchorBeanFactory
AnchorCheckedException - Exception in org.anchoranalysis.core.exception: A base class for all checked exceptions used on the Anchor platform
AnchorCheckedException() - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
AnchorCheckedException(String) - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
AnchorCheckedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
AnchorCheckedException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
AnchorCombinableException - Exception in org.anchoranalysis.core.exception.combinable: An exception that can be combined with similar exceptions and summarized.
AnchorCombinableException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
AnchorDefaultBeanFactory - Class in org.anchoranalysis.bean.xml.factory: The default bean factory used for initializing AnchorBeans
AnchorDefaultBeanFactory(BeanInstanceMap) - Constructor for class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
AnchorFriendlyCheckedException - Exception in org.anchoranalysis.core.exception.friendly: A base class for particular checked-exceptions which are guaranteed to provide a user-friendly error description.
AnchorFriendlyCheckedException(String) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException: A user-friendly error message WITHOUT a cause.
AnchorFriendlyCheckedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException: A user-friendly error message and its cause.
AnchorFriendlyCheckedException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException: A wrapped exception.
AnchorFriendlyRuntimeException - Exception in org.anchoranalysis.core.exception.friendly: A base class for particular runtime-exceptions which are guaranteed to provide a user-friendly error description.
AnchorFriendlyRuntimeException(String) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException: A user-friendly error message WITHOUT a cause.
AnchorFriendlyRuntimeException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException: A user-friendly error message and its cause.
AnchorFriendlyRuntimeException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException: A wrapped exception.
AnchorImpossibleSituationException - Exception in org.anchoranalysis.core.exception.friendly: A run-time exception to throw in situations which should never occur, instead of
AnchorImpossibleSituationException() - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorImpossibleSituationException
AnchorNeverOccursException - Exception in org.anchoranalysis.core.exception: This is an exceotion that should never be thrown, but can be used for type-safety where an exception is needed
AnchorNeverOccursException() - Constructor for exception org.anchoranalysis.core.exception.AnchorNeverOccursException
AnchorRuntimeException - Exception in org.anchoranalysis.core.exception: A base class for all unchecked (runtime) exceptions used on the Anchor platform
AnchorRuntimeException() - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
AnchorRuntimeException(String) - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
AnchorRuntimeException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
AnchorRuntimeException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
And - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation and voxelwise on both masks, modifying {mask} with the result.
And - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: Applies multiples filter with logical AND i.e.
And() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.And
And() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.And
AndCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: Combines two UpdatableBeforeConditions as LOGICAL ANDs
AndCondition(UpdatableBeforeCondition, UpdatableBeforeCondition) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
AndKernel - Class in org.anchoranalysis.image.voxel.kernel
AndKernel(BinaryKernel, BinaryKernel) - Constructor for class org.anchoranalysis.image.voxel.kernel.AndKernel
AndList - Class in org.anchoranalysis.plugin.mpp.bean.check
AndList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.AndList
AndObjectsWithMasks - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask: Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
AndObjectsWithMasks() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
AngleRotation - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
AngleRotation() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
AnisotropicDiffusion - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider: Perona-Malik Anisotropic Diffusion
AnisotropicDiffusion() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
AnnealScheme - Class in org.anchoranalysis.mpp.bean.anneal
AnnealScheme() - Constructor for class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
Annotation - Interface in org.anchoranalysis.annotation: Base class for types of image annotations.
AnnotationAggregateCSVGenerator - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
AnnotationAggregateCSVGenerator() - Constructor for class org.anchoranalysis.plugin.annotation.bean.aggregate.AnnotationAggregateCSVGenerator
AnnotationBackground - Class in org.anchoranalysis.annotation.io.bean
AnnotationBackground() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotationBackground
AnnotationComparisonAssigner<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
AnnotationComparisonAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
AnnotationComparisonInput<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.comparison
AnnotationComparisonInput(T, Tuple2<Comparer, Comparer>, Tuple2<String, String>, StackReader) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
AnnotationComparisonInputManager<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
AnnotationComparisonInputManager() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
AnnotationDeleter - Interface in org.anchoranalysis.annotation.io
annotationExistsCorrespondTo(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
AnnotationGroup<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.comparison
AnnotationGroup(String) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
AnnotationGroupList<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.comparison
AnnotationGroupList() - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
AnnotationGroupObject - Class in org.anchoranalysis.plugin.annotation.comparison
AnnotationGroupObject(String) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
AnnotationInputManager<T extends ProvidesStackInput,S extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io.bean
AnnotationInputManager() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
AnnotationLabel - Class in org.anchoranalysis.plugin.annotation.bean.label
AnnotationLabel() - Constructor for class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
annotationLabelFor(ProvidesStackInput) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: Returns a label describing the annotation, or empty() if this makes no sense
annotationLabelFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
annotationLabelFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
AnnotationMarksComparer<T> - Class in org.anchoranalysis.plugin.annotation.bean.comparer
AnnotationMarksComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
annotationPathFor(ProvidesStackInput) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
annotationPathFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
AnnotationReader<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
AnnotationWithMarks - Interface in org.anchoranalysis.annotation.mark: An image-annotation that involves a mark-collection.
AnnotationWithStrategy<T extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io: An annotation that has been combined with its strategy.
AnnotationWithStrategy(ProvidesStackInput, T) - Constructor for class org.anchoranalysis.annotation.io.AnnotationWithStrategy
AnnotationWriter<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
AnnotatorStrategy - Class in org.anchoranalysis.annotation.io.bean
AnnotatorStrategy() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
Anonymize - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming: Copies files to a number 001 002 etc.
Anonymize() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
any() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper: Returns voxels that are not cast to any specific buffer type
anyDimensionIsLargerThan(Extent) - Method in class org.anchoranalysis.spatial.Extent: Returns true if any dimension in this extent is larger than the corresponding dimension in other extent
anyExists() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
anyExists() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
anyExists() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Does at least one value satisfy the predicate - across all voxels?
anyMatch(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Does the predicate evaluate to true on any object in the collection?
anyPredicateMatch(Voxels<T>, Predicate<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Tries to apply a predicate to all the remaining buffer locations, returning true if the predicate matches.
AnySliceCenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check: The center ps of at least one slice should be on the stack Tries overall center point first, and then projects it onto each slice
AnySliceCenterOnMask() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.AnySliceCenterOnMask
append(Optional<FeatureList<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Appends one or more additional (optional) feature-lists
AppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: A CSV that is appended from the root of a project
AppendCsv() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv
AppendFilePath - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendFilePath() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendFilePath
AppendHistogram - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendHistogram() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
AppendKeyValueParams - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendKeyValueParams() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
AppendMarks - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendMarks() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendMarks
AppendObjects - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
AppendObjects() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendObjects
AppendStack - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: A stack from a stack-collection
AppendStack() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
AppendStackDirect - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: A stack from a stack-collection
AppendStackDirect() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
apply(int) - Method in interface org.anchoranalysis.core.functional.checked.CheckedIntFunction: Calls the function
apply(int, int) - Method in interface org.anchoranalysis.core.functional.checked.IntBinaryOperation
apply(Integer) - Method in class org.anchoranalysis.core.index.IndexBridge
apply(String, Path) - Static method in class org.anchoranalysis.io.generator.text.WriteStringToFile
apply(Throwable, Writer, String, int, boolean) - Static method in class org.anchoranalysis.core.exception.friendly.RecursivelyDescribeExceptionStack: Incrementally adds a line to a string builder with the message of each exception moving onto the next nested exception until there are no more
apply(IFormatReader, ReadOptions, int) - Method in class org.anchoranalysis.io.bioformats.DimensionsCreator
apply(ImageInitParams) - Static method in class org.anchoranalysis.image.bean.nonbean.init.CreateCombinedStack
apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskAnd: Performs a AND operation on each voxel in two masks, writing the result onto the second mask.
apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskIfHighLow: Performs a iff first==HIGH and second==LOW then LOW operation on each voxel in two masks, writing the result onto the second mask.
apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskOr: Performs a OR operation on each voxel in two masks, writing the result onto the first mask.
apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskXor: Performs a XOR (exclusive OR) operation on each voxel in two masks, writing the result onto the first mask.
apply(BinaryKernel, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
apply(BinaryKernel, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
apply(ObjectMask, double, int, int) - Static method in class org.anchoranalysis.plugin.points.bean.contour.SplitContourSmoothingSpline: 1.
apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskAnd: Performs a AND operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.
apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskXor: Performs a XOR (exclusive OR) operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.
apply(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedFunction: Calls the function
apply(S, T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedBiFunction: Calls the function
apply(T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedUnaryOperator
applyAsDouble(T, U) - Method in interface org.anchoranalysis.core.functional.checked.CheckedToDoubleBiFunction: Applies this function to the given arguments.
applyAsInt(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedToIntFunction: Calls the function
applyCoefficientsToMark(DoubleMatrix2D, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
applyDelta(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta: Applies the changes to enable or disable additional outputs, if they are defined.
applyFitResultToMark(Ellipsoid, Dimensions, double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
applyForCount(BinaryKernel, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
applyForCount(CountKernel, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Applies the kernel to voxels and sums the returned value
applyForCount(CountKernel, Voxels<UnsignedByteBuffer>, BoundingBox) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Applies the kernel to voxels and sums the returned value
applyForCountOnMask(BinaryKernel, Voxels<UnsignedByteBuffer>, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
applyGlobal(List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.OutlineTraverser: Root point is arbitrarily chosen from object
applyGlobal(Point3i, List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.OutlineTraverser
ApplyImageJMorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.mask: Applies an ImageJ (2D) morphological operation to voxels
applyInitializationIfPossibleTo(Object, Object, Logger) - Method in class org.anchoranalysis.bean.initializable.property.PropertyInitializer: Applies the initialization to a property using the current or extracted params if possible.
ApplyKernel - Class in org.anchoranalysis.image.voxel.kernel: Applies a kernel to a Voxel Box
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
applyOperation(Dimensions, UnaryOperator<Stack>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks: Applies an operation on each stack in the collection and returns a new derived collection
applyOperation(BinaryVoxels<UnsignedByteBuffer>, String, int) - Static method in class org.anchoranalysis.plugin.imagej.mask.ApplyImageJMorphologicalOperation
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
ApplyPermutations<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.permute: Applies a PermuteProperty to a bean to create new duplicated beans each with a permutation
ApplyPermutations(ApplyPermutations.NameGetter<T>, ApplyPermutations.NameSetter<T>) - Constructor for class org.anchoranalysis.bean.permute.ApplyPermutations
ApplyPermutations.NameGetter<S> - Interface in org.anchoranalysis.bean.permute
ApplyPermutations.NameSetter<S> - Interface in org.anchoranalysis.bean.permute
applyPermutationsToCreateDuplicates(List<T>, PermuteProperty<S>, PermutationSetter) - Method in class org.anchoranalysis.bean.permute.ApplyPermutations: Takes a list of beans, and creates a permuted version, updating the custom names
applyRadiiSubtractScale(double, double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
applyRankFilter(Channel, int, int) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper: Applies a 2D rank-filter to each slice independently.
ApplyRegExSubstitution - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming: A regular expression substitution (replaceAll) is applied to the relative-path
ApplyRegExSubstitution() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
applyStrategy(MergeCandidate) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeStrategy
applyUntilPositive(CountKernel, Voxels<UnsignedByteBuffer>, BoundingBox) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Applies the kernel to voxels until a positive value is returned, then exits with true
ArbitraryInsidePoint - Class in org.anchoranalysis.plugin.image.feature.bean.object.single: Calculates deterministicly a point that is definitely inside the object-mask.
ArbitraryInsidePoint() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
ArbitraryInsidePoint(String) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
ArbitraryPointCommon - Class in org.anchoranalysis.mpp.feature.addcriteria: If one arbitrarily point overlaps between two MarkPointList then true, otherwise false
ArbitraryPointCommon() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
Area<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Area of the stack (XY dimensions only, Z dimension is not considered)
Area() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Area
areAllPointsInBigNeighborhood(List<Point3i>) - Static method in class org.anchoranalysis.image.core.points.PointsNeighborChecker: Are all points in a list neighboring the next point in the list?
AreaPhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.area: Area expressed in physical coordinates
AreaPhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
AreaPixels - Class in org.anchoranalysis.image.bean.unitvalue.extent.area: Area expressed as square pixels
AreaPixels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
AreaPixels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
areEqual(double, double) - Static method in class org.anchoranalysis.math.arithmetic.DoubleUtilities: Are the two numbers equal?
areEqual(float, float) - Static method in class org.anchoranalysis.math.arithmetic.FloatUtilities: Are the two numbers equal?
areNeighborsDistinct(List<Point3i>) - Static method in class org.anchoranalysis.image.core.points.PointsNeighborChecker: Makes sure no successive neighbors are equal
arePointsNeighbors(Point3i, Point3i) - Static method in class org.anchoranalysis.image.core.points.PointsNeighborChecker
areXmlEqual(Document, Document) - Static method in class org.anchoranalysis.test.TestLoader: Does a check if the XML documents are equal
ArgumentConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path: Converts string passed as arguments.
arithmetic() - Method in class org.anchoranalysis.image.core.channel.Channel
arithmetic() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
arithmetic() - Method in class org.anchoranalysis.image.voxel.Voxels: Methods to manipulate the voxel-values via arithmetic
arithmetic() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
ArithmeticWithConstantBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Base-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.
ArithmeticWithConstantBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
ArithmeticWithConstantConditionallyWriteBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
ArithmeticWithConstantConditionallyWriteBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
ArrangeRaster - Class in org.anchoranalysis.image.bean.provider.stack: Creates a stack that tiles (or otherwise combines) other providers
ArrangeRaster() - Constructor for class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
ArrangeStack - Interface in org.anchoranalysis.image.bean.nonbean.spatial.arrange
ArrangeStackBean - Class in org.anchoranalysis.image.bean.spatial.arrange
ArrangeStackBean() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.ArrangeStackBean
ArrangeStackException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange
ArrangeStackException(Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException
ArrangeStackException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException
array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: The array of the buffer ala ByteBuffer.array().
array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: The array of the buffer ala ShortBuffer.array().
asByte() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
asByte(ImageProcessor) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToVoxelBuffer: Convert a ImageProcessor to VoxelBuffer<UnsignedByteBuffer>
asByteOrCreateEmpty(boolean) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper: Reuses the existing buffer if byte, otherwise creates a new empty byte buffer
AsCollection - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
AsCollection() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsCollection
asCollectionOrderNotPreserved() - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements: Returns the scaled-elements as a collection but without preserving the original element order.
asExtent() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Creates an extent with identical width and height and depth (z-extent) of 1
asExtent(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Creates an extent with identical width and height and a specific depth (z-extent)
asFloat() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
asInt() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
asList() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
asList() - Method in class org.anchoranalysis.feature.name.FeatureNameList
asList() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Exposes the underlying objects as a list
asList() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
asList() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
asListChannels() - Method in class org.anchoranalysis.image.core.stack.Stack
asListOrderPreserved(List<T>) - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements: Returns a list of scaled-elements corresponding to a list of unscaled-elements
asMap() - Method in class org.anchoranalysis.core.identifier.name.MapCreate
AsMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
AsMark() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
asMarks() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
AsObject - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
AsObject() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
AsObjectMask - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object: Treats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask feature
AsObjectMask() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
asObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
asOperationFailedException() - Method in exception org.anchoranalysis.core.index.GetOperationFailedException
asOrderedArray() - Method in class org.anchoranalysis.spatial.Extent
asPath() - Method in class org.anchoranalysis.bean.shared.path.RootPath
asPoint() - Method in class org.anchoranalysis.image.bean.spatial.Padding
assertCalc(ResultsVector, Object...) - Static method in class org.anchoranalysis.test.feature.plugins.ResultsVectorTestUtilities
assertDoubleResult(String, Feature<T>, T, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
assertDoubleResult(String, Feature<T>, T, Optional<SharedObjects>, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
assertDoubleResult(String, Feature<T>, T, T, double, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculatorDuo
assertIntResult(String, Feature<T>, T, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
assertIntResult(String, Feature<T>, T, Optional<SharedObjects>, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
assertIntResult(String, Feature<T>, T, T, int, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculatorDuo
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
assertValid() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
asShort() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
asShort(ImageProcessor) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToVoxelBuffer: Convert a ImageProcessor to VoxelBuffer<UnsignedShortBuffer>
assignAccepted(DualMarks) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Assigns marks with an overall accepted state.
assignBestFromCurrent() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
assignBoundingBox(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundedList: Assigns a new containing bounding-box.
assignBoundingBoxAndMap(BoundingBox, UnaryOperator<T>) - Method in class org.anchoranalysis.spatial.box.BoundedList: Assigns a new containing bounding-box and maps each individual element.
assignCurrent(Optional<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
assignDescription(ManifestDirectoryDescription) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory: Assigns a description, which may not already exist.
assignEachMatchingPoint(Voxels<?>, IntPredicate, int) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Assigns a value to any voxel whose intensity matches a predicate, reading and writing the buffer as an int.
assignFrom(CachedSupplierBase<T>) - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
assignFrom(Mark) - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: Assigns a new mark to replace the existing mark.
AssignFromChannel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Copies the pixels from channelAssignFrom to channel (possibly masking)
AssignFromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
AssignFromIntersectingObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Matches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target object
AssignFromIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
AssignFromParams - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
AssignFromParams() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
assignFunction(String) - Method in class org.anchoranalysis.io.manifest.ManifestDescription: Assigns a new function.
assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType: If the sequence-type supports a different maximum-index to that derived from the elements SequenceType.update(T), this assigns it.
assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
Assignment - Interface in org.anchoranalysis.annotation.io.assignment
AssignmentGenerator - Class in org.anchoranalysis.annotation.io.assignment.generator: Outputs a raster showing an Assignment on a background.
AssignmentGenerator(DisplayStack, IntFunction<ColorPool>, boolean, Tuple2<String, String>, boolean, int) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
AssignmentMaskIntersection - Class in org.anchoranalysis.annotation.io.assignment: Calculates statistics (DICE, Jaccard etc.) based upon corresponding two object-masks
AssignmentMaskIntersection(ObjectMask, ObjectMask) - Constructor for class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
AssignmentObjectFactory - Class in org.anchoranalysis.annotation.io.assignment
AssignmentObjectFactory(FeatureEvaluator<FeatureInputPairObjects>, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.AssignmentObjectFactory
AssignmentOverlapFromPairs - Class in org.anchoranalysis.annotation.io.assignment: Pairs objects in left with objects in right
AssignmentOverlapFromPairs() - Constructor for class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
AssignMode<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode: How assignments and other decisions are made in the SimulatedAnnealing optimizaton
AssignMode() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
assignOff() - Method in class org.anchoranalysis.image.core.mask.Mask
assignOff() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
assignOff() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Assigns OFF value to voxels, expecting global coordinates
assignOn() - Method in class org.anchoranalysis.image.core.mask.Mask
assignOn() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
assignOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Assigns ON value to voxels, expecting global coordinates
assignParentFolder(Optional<MutableDirectory>) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
assignPath(Path) - Method in class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
assignPaused(DualMarks) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Assigns marks with an overall paused state.
assignPriority(ObjectVertex, ObjectVertex, GraphLogger) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority: Assigns a priority to a potential merge
AssignPriority - Class in org.anchoranalysis.plugin.image.object.merge.priority
AssignPriority() - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority
AssignPriorityFromImprovement - Class in org.anchoranalysis.plugin.image.object.merge.priority: Allows merges if there is an increase in the payload i.e.
AssignPriorityFromImprovement(PayloadCalculator) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromImprovement
AssignPriorityFromPair - Class in org.anchoranalysis.plugin.image.object.merge.priority: Calculates pair-feature on each potential merge, and this value determines priority..
AssignPriorityFromPair(FeatureCalculatorSingle<FeatureInputPairObjects>, double, RelationToValue) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromPair
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromImprovement
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromPair
assignProposal(Optional<T>, KernelWithIdentifier<S>) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
assignProposal(OptimizationStep<S, T>, TransformationContext, KernelWithIdentifier<S>) - Method in interface org.anchoranalysis.mpp.segment.kernel.KernelAssigner
assignProposal(OptimizationStep<S, T>, TransformationContext, KernelWithIdentifier<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerAddErrorLevel
assignProposal(OptimizationStep<S, T>, TransformationContext, KernelWithIdentifier<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerCalculateEnergyFromKernel
assignRejected(DualMarks, T) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Assigns marks with an overall rejected state.
assignType(String) - Method in class org.anchoranalysis.io.manifest.ManifestDescription: Assigns a new type.
assignValue(int) - Method in class org.anchoranalysis.image.core.channel.Channel
assignValue(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Assigns a value to a bounded-voxels accepting global coordinates for objects, boxes etc.
assignValue(int) - Method in class org.anchoranalysis.image.voxel.Voxels: Provides a means to assign a constant-value to some or all of the voxels
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsAsFloat
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsAsInt
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsAsShort
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
AssignValue - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign: Assigns a constant (scalar) value to the portion of the image covered by a mask
AssignValue() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
AsSingle - Class in org.anchoranalysis.mpp.feature.bean.energy.element: Extracts one of the memos from the pair, and processes as a FeatureSingleMemo
AsSingle() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
AsSingleMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
AsSingleMark() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsSingleMark
associatedFile() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
associateXml(XMLConfiguration) - Method in interface org.anchoranalysis.bean.xml.AssociateXmlUponLoad: Associated
associateXml(XMLConfiguration) - Method in class org.anchoranalysis.experiment.bean.Experiment
associateXml(XMLConfiguration) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
AssociateXmlUponLoad - Interface in org.anchoranalysis.bean.xml: For classes that wish to have a XmlConfiguration associated with them
asStack() - Method in class org.anchoranalysis.feature.energy.EnergyStack
asStack() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
asStack() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
asTuple() - Method in class org.anchoranalysis.spatial.Extent: Exposes the extent as a tuple.
asVoxels() - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer: The target buffer
atanHandlingNan(double) - Static method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
atBorder(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
AtBorderBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
AtBorderBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
atBorderXY(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
AtBorderXY - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
AtBorderXY() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderXY
atBorderZ(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
AtBorderZ - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
AtBorderZ() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderZ
atCorner(ReadableTuple3i, VoxelsExtracter<T>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Projects a VoxelsExtracter to a corner in a larger global space
AtIndex - Class in org.anchoranalysis.plugin.image.bean.object.provider: Creates a new object-collection with only a single element (at a particular index) in the existing collection.
AtIndex() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
AtLeastZSlices - Class in org.anchoranalysis.plugin.io.bean.groupfiles.check
AtLeastZSlices() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
AtScale - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Perform a segmentation at a different scale, and then fit the results back to the original scale.
AtScale() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
attachObject(Channel) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
attachObject(S) - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached
AutoLocalThreshold - Class in org.anchoranalysis.plugin.fiji.bean.mask.provider: Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
AutoLocalThreshold() - Constructor for class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
Autoname - Class in org.anchoranalysis.plugin.io.bean.channel.map: Names of the channels from the metadata if it exists, or after RGB, or by index
Autoname() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.Autoname
AxisAlignedUnitVector - Class in org.anchoranalysis.image.bean.spatial.direction
AxisAlignedUnitVector() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
AxisLimits - Class in org.anchoranalysis.plot
AxisLimits() - Constructor for class org.anchoranalysis.plot.AxisLimits
AxisLimits(double, double) - Constructor for class org.anchoranalysis.plot.AxisLimits
AxisRatioEllipsoid - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
AxisRatioEllipsoid() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.AxisRatioEllipsoid
AxisType - Enum in org.anchoranalysis.spatial.axis
AxisTypeConverter - Class in org.anchoranalysis.spatial.axis: Converts to/from AxisType to string representations and integer index (0 for X, 1 for Y, 2 for Z)
AxisTypeException - Exception in org.anchoranalysis.spatial.axis
AxisTypeException(String) - Constructor for exception org.anchoranalysis.spatial.axis.AxisTypeException

B

background() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
background(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksFlattenedGenerator
background(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGenerator
background(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
BackgroundCreator - Class in org.anchoranalysis.mpp.io.output
backgroundStack() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
BackgroundSubtractor - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider
BackgroundSubtractor() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor
BarPlot<T> - Class in org.anchoranalysis.plot.index: A bar plot, stacked or non-stacked.
BarPlot(String, String[], GetForSeries<T, String>, GetForSeries<T, Double>, GetForSeries<T, Paint>, boolean) - Constructor for class org.anchoranalysis.plot.index.BarPlot
Base<T> - Class in org.anchoranalysis.image.voxel.extracter
Base(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.extracter.Base
BASE - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
BBoxRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
BBoxRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.BBoxRatio
BeanDuplicateException - Exception in org.anchoranalysis.bean.error: An exception occurs when the duplication of a bean fails
BeanDuplicateException(Exception) - Constructor for exception org.anchoranalysis.bean.error.BeanDuplicateException
BeanDuplicateException(String) - Constructor for exception org.anchoranalysis.bean.error.BeanDuplicateException
BeanDuplicateException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.error.BeanDuplicateException
BeanField - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a field in an Anchor Bean class is to be treated as a bean-field.
beanFor(Field, AnchorBean<?>) - Static method in class org.anchoranalysis.bean.permute.setter.PermutationSetterUtilities: Finds a bean corresponding to a field (exceptionally handling a List by taking the first item in it)
BeanInitParams - Interface in org.anchoranalysis.bean.initializable.params: Parent class for all parameters used to initialise beans in InitializableBean
BeanInstanceMap - Class in org.anchoranalysis.bean: Maps a AnchorBean family-type to some beans belong to the family.
BeanInstanceMap() - Constructor for class org.anchoranalysis.bean.BeanInstanceMap
BeanMisconfiguredException - Exception in org.anchoranalysis.bean.error: If a Bean is misconfigured
BeanMisconfiguredException(String) - Constructor for exception org.anchoranalysis.bean.error.BeanMisconfiguredException
BeanMisconfiguredException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.error.BeanMisconfiguredException
BeanMisconfiguredXmlException - Exception in org.anchoranalysis.bean.xml.error: A bean's XML is thrown when a bean has misconfigured XML
BeanMisconfiguredXmlException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException: Constructor
BeanMisconfiguredXmlException(Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException: Constructor
BeanPathUtilities - Class in org.anchoranalysis.bean.xml.factory
BeanProviderAsStackBase<T,S> - Class in org.anchoranalysis.image.bean.provider: A provider base-class that as well as providing type S, also provide a stack
BeanProviderAsStackBase() - Constructor for class org.anchoranalysis.image.bean.provider.BeanProviderAsStackBase
BeanStoreAdder - Class in org.anchoranalysis.bean.store
BeanStrangeException - Exception in org.anchoranalysis.bean.error: When something quite strange happens that we don't usually want to catch.
BeanStrangeException(String) - Constructor for exception org.anchoranalysis.bean.error.BeanStrangeException
BeanStrangeException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.error.BeanStrangeException
BeanTestChecker - Class in org.anchoranalysis.test.experiment: Checks to see if a bean has been misconfigured, when created manually in tests (thereby skipping the usual checks during the BeanXML loading process).
BeanXmlException - Exception in org.anchoranalysis.bean.xml.error: An exception that occurs when one cannot process BeanXML for some reason
BeanXmlException(String) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanXmlException
BeanXmlException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanXmlException
BeanXmlException(Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanXmlException
BeanXmlLoader - Class in org.anchoranalysis.bean.xml: Creates beans based on XML specifying their properties (including nested children).
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.task.Task: Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.feature.bean.Feature: Dummy method, that children can optionally override
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
beforeCalcWithImageInitParams(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
beforeCalcWithImageInitParams(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
beforeCalcWithImageInitParams(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
BeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
beforeCopying(Path, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
beforeCopying(Path, int) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming
beforeCopying(Path, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
beforeCopying(Path, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
BidirectionalBound - Class in org.anchoranalysis.mpp.bound
BidirectionalBound(Optional<ResolvedBound>, Optional<ResolvedBound>) - Constructor for class org.anchoranalysis.mpp.bound.BidirectionalBound
BinaryClassifierImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
BinaryClassifierImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
BinaryKernel - Class in org.anchoranalysis.image.voxel.kernel
BinaryKernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.BinaryKernel
BinaryKernelMorph3 - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
BinaryKernelMorph3(BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
BinaryKernelMorph3Extent - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
BinaryKernelMorph3Extent(BinaryValuesByte, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent
BinaryNotOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects anything that is not off voxels from a binary mask.
BinaryNotOffVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
BinaryNotOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects anything that is not on voxels from a binary mask.
BinaryNotOnVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
BinaryOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects only the off voxels from a binary mask.
BinaryOffVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
BinaryOnOffSetter - Interface in org.anchoranalysis.image.voxel.binary
BinaryOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects only the on pixels from a binary mask.
BinaryOnVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
binaryOperation(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, IntBinaryOperation) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in a bounding-box - applying a binary operation with values from two input Voxels<UnsignedByteBuffer> for each slice and writing it into an output Voxels<UnsignedByteBuffer>.
BinaryOutcomeImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
BinaryOutcomeImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
binaryResizing(int) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
BinarySegmentation - Class in org.anchoranalysis.image.bean.segment.binary
BinarySegmentation() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentation
BinarySegmentationOne - Class in org.anchoranalysis.image.bean.segment.binary
BinarySegmentationOne() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
BinarySegmentationParameters - Class in org.anchoranalysis.image.bean.nonbean.segment: Parameters that are optionally associated with a BinarySegmentation
BinarySegmentationParameters() - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
BinarySegmentationParameters(Optional<Resolution>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
BinarySegmentationParameters(Optional<Histogram>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
BinarySegmentationParameters(Resolution, Optional<Histogram>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: Constructor
BinarySegmentationReference - Class in org.anchoranalysis.image.bean.segment.binary
BinarySegmentationReference() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
binarySegmentations() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
BinarySegmentationThreshold - Class in org.anchoranalysis.image.bean.segment.binary
BinarySegmentationThreshold() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
BinarySegmentByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Performs a binary-segmentation using the upstream objects as masks.
BinarySegmentByObject() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
binaryValues() - Method in class org.anchoranalysis.image.core.mask.Mask
binaryValues() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Which two intensity values represent OFF and ON states
binaryValues() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
BinaryValues - Class in org.anchoranalysis.image.voxel.binary.values: Two values representing int binary states in an unsigned-byte buffer e.g.
BinaryValues(int, int) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValues
binaryValuesByte() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
BinaryValuesByte - Class in org.anchoranalysis.image.voxel.binary.values: Two values representing byte binary states in an unsigned-byte buffer e.g.
BinaryValuesByte(byte, byte) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
BinaryValuesByte(int, int) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
binaryVoxels() - Method in class org.anchoranalysis.image.core.mask.Mask
binaryVoxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
BinaryVoxels<T> - Class in org.anchoranalysis.image.voxel.binary: Like Voxels but should only contain two distinct intensity-values representing ON and OFF states.
BinaryVoxels(Voxels<T>, BinaryValues) - Constructor for class org.anchoranalysis.image.voxel.binary.BinaryVoxels
BinaryVoxelsBase - Class in org.anchoranalysis.image.bean.threshold.relation
BinaryVoxelsBase() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
BinaryVoxelsFactory - Class in org.anchoranalysis.image.voxel.binary
binaryVoxelsFor(Voxels<T>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
bind(FeatureList<T>, FeatureInitParams, SharedFeatureMulti, Logger) - Method in class org.anchoranalysis.feature.session.strategy.replace.bind.BoundReplaceStrategy
BindFailedException - Exception in org.anchoranalysis.io.output.outputter
BindFailedException(String) - Constructor for exception org.anchoranalysis.io.output.outputter.BindFailedException
BindFailedException(Throwable) - Constructor for exception org.anchoranalysis.io.output.outputter.BindFailedException
BioformatsOpenedRaster - Class in org.anchoranalysis.io.bioformats
BioformatsOpenedRaster(IFormatReader, IMetadata, ReadOptions) - Constructor for class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
BioformatsReader - Class in org.anchoranalysis.io.bioformats.bean
BioformatsReader() - Constructor for class org.anchoranalysis.io.bioformats.bean.BioformatsReader
BioformatsReader(ReadOptions) - Constructor for class org.anchoranalysis.io.bioformats.bean.BioformatsReader
BioformatsWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats: Base class for writing a stack to the filesystem using the Bioformats library.
BioformatsWriter() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter
bitDepth() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
bitDepth() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
BitDepth - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
BitDepth() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
BlackBackgroud - Class in org.anchoranalysis.plot.bean.colorscheme: A black background and white axes.
BlackBackgroud() - Constructor for class org.anchoranalysis.plot.bean.colorscheme.BlackBackgroud
blockUntilLoaded() - Static method in class org.anchoranalysis.plugin.opencv.CVInit: Blocks a thread until the initialization has completed.
blue() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
blur(VoxelsWrapper, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurGaussian3D
blur(VoxelsWrapper, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurGaussianEachSlice2D
blur(VoxelsWrapper, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
Blur - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
Blur() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
BlurGaussian3D - Class in org.anchoranalysis.plugin.image.bean.blur: Performs a Gaussian Blur in 3D
BlurGaussian3D() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurGaussian3D
BlurGaussianEachSlice2D - Class in org.anchoranalysis.plugin.image.bean.blur: Performs a Gaussian-blur in 2D on each slice independently
BlurGaussianEachSlice2D() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurGaussianEachSlice2D
BlurStrategy - Class in org.anchoranalysis.plugin.image.bean.blur: A method for applying blurring to an image
BlurStrategy() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
bothNameAndParams() - Static method in class org.anchoranalysis.feature.list.NamedFeatureStoreFactory
Bound - Class in org.anchoranalysis.mpp.bean.bound
Bound() - Constructor for class org.anchoranalysis.mpp.bean.bound.Bound
boundaryMax(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
boundaryMax(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Boundary to define the maximum accepted value in the range
boundaryMax(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
boundaryMin(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
boundaryMin(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Boundary to define the minimum accepted value in the range
boundaryMin(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
BoundCalculator - Class in org.anchoranalysis.mpp.bean.bound
BoundCalculator() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundCalculator
BoundCalculatorException - Exception in org.anchoranalysis.mpp.bound
BoundCalculatorException(Exception) - Constructor for exception org.anchoranalysis.mpp.bound.BoundCalculatorException
BoundCalculatorException(String) - Constructor for exception org.anchoranalysis.mpp.bound.BoundCalculatorException
boundChanged(BoundChangeEvent) - Method in interface org.anchoranalysis.core.index.bounded.BoundChangeListener
BoundChangeEvent - Class in org.anchoranalysis.core.index.bounded
BoundChangeEvent(Object, BoundChangeEvent.BoundType) - Constructor for class org.anchoranalysis.core.index.bounded.BoundChangeEvent
BoundChangeEvent.BoundType - Enum in org.anchoranalysis.core.index.bounded
BoundChangeListener - Interface in org.anchoranalysis.core.index.bounded
BoundDegrees - Class in org.anchoranalysis.mpp.bean.bound
BoundDegrees() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundDegrees
BoundDegrees(BoundDegrees) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundDegrees
BoundedIndexContainer<T> - Interface in org.anchoranalysis.core.index.bounded
BoundedIndexContainerBridge<H,S,E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge: Bridges calls from hidden-type to external-type.
BoundedIndexContainerBridge(BoundedIndexContainer<H>) - Constructor for class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
BoundedIndexContainerBridgeWithIndex<H,S,E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge: Bridges calls from hidden-type to external-type.
BoundedIndexContainerBridgeWithIndex(BoundedIndexContainer<H>, BridgeElementWithIndex<H, S, E>) - Constructor for class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithIndex
BoundedIndexContainerBridgeWithoutIndex<H,S,E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge: Bridges calls from hidden-type to external-type.
BoundedIndexContainerBridgeWithoutIndex(BoundedIndexContainer<H>, CheckedFunction<H, S, E>) - Constructor for class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithoutIndex
BoundedIndexContainerFromList<T> - Class in org.anchoranalysis.core.index.bounded
BoundedIndexContainerFromList(List<T>) - Constructor for class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
BoundedList<T> - Class in org.anchoranalysis.spatial.box: One or more elements, each with an individual bounding-box, and collectively with a bounding-box that fully contains them all.
BoundedRange - Interface in org.anchoranalysis.core.index.bounded
BoundedRangeIncomplete - Interface in org.anchoranalysis.core.index.bounded: A range of discrete integers that is not complete (missing many integers).
BoundedRangeIncompleteDynamic - Interface in org.anchoranalysis.core.index.bounded
boundedVoxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
BoundedVoxels<T> - Class in org.anchoranalysis.image.voxel: Voxel-data that is bounded to exist in a particular bounding-box in an image.
BoundedVoxels(BoundedVoxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels: Copy constructor
BoundedVoxels(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels: Creates voxels bounded to match the entire voxel-data at the origin.
BoundedVoxels(BoundingBox, Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels: Creates voxels with a corresponding bounding box.
BoundedVoxelsFactory - Class in org.anchoranalysis.image.voxel
boundingBox() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
boundingBox() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A bounding-box that associates voxels to a particular part of an image
boundingBox() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
boundingBox() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: A bounding-box enclosing the voxelized representation of the mark
boundingBox() - Method in class org.anchoranalysis.spatial.box.BoundedList: A bounding-box that must contain all elements in the collection
BoundingBox - Class in org.anchoranalysis.spatial.box: A bounding-box in 2 or 3 dimensions.
BoundingBox(Extent) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox: Constructs a bounding-box to cover the entirety of a certain extent.
BoundingBox(Point3d, Point3d) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox: Creates from two double points (a minimum corner and a maximum corner).
BoundingBox(ReadableTuple3i, Extent) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox
BoundingBox(ReadableTuple3i, ReadableTuple3i) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox: Creates from two int points (a minimum corner and a maximum corner).
BoundingBoxAlongAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxAlongAxisBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
BoundingBoxCalculator - Class in org.anchoranalysis.mpp.mark.conic: Functions to calculate a bounding-box for a point surrounded by some form of radii
BoundingBoxContains - Class in org.anchoranalysis.spatial.box: Does a bounding box contain other objects? e.g.
BoundingBoxContains(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxContains
BoundingBoxDistance - Class in org.anchoranalysis.spatial.box: Calculates distance between two bounding boxes
BoundingBoxesOnPlane - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange: Describes a set of bounding boxes on top of a plane
BoundingBoxesOnPlane(Extent) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
BoundingBoxesOnPlane(Extent, BoundingBox) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
BoundingBoxExtent - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
BoundingBoxExtent() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
BoundingBoxExtentAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxExtentAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxExtentAlongAxis
boundingBoxFlattened() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: The bounding-box flattened in z dimension
boundingBoxFor(T) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask: A bounding-box for a given element.
boundingBoxForRegion(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
BoundingBoxFromPoints - Class in org.anchoranalysis.image.core.points: Creates a bounding-box from one or more points
BoundingBoxIntersection - Class in org.anchoranalysis.mpp.feature.addcriteria
BoundingBoxIntersection - Class in org.anchoranalysis.spatial.box: Methods for checking intersection between a particular bounding-box and others
BoundingBoxIntersection() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
BoundingBoxIntersection(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxIntersection
BoundingBoxMaximumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxMaximumAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMaximumAlongAxis
BoundingBoxMerger - Class in org.anchoranalysis.spatial.box
BoundingBoxMinimumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxMinimumAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMinimumAlongAxis
BoundingBoxNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
BoundingBoxNumberVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxNumberVoxels
boundingBoxThatSpansInput(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
boundingBoxThatSpansInput(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
boundingBoxThatSpansInput(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Creates a bounding-box that tightly fits the input to a particular table row (could be for one or more objects)
BoundingBoxUnion - Class in org.anchoranalysis.spatial.box: Performs union of a bounding-box with other entities
BoundingBoxUnion(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxUnion
BoundingBoxZDistance - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance: Measures the amount of distance in Z for the bounding box.
BoundingBoxZDistance() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZDistance
BoundingBoxZOverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance: Measures the amount of bounding box overlap in the Z dimension
BoundingBoxZOverlapRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
BoundMinMax - Class in org.anchoranalysis.mpp.bean.bound
BoundMinMax() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax
BoundMinMax(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax
BoundMinMax(BoundMinMax) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax
BoundOutputter<T> - Class in org.anchoranalysis.io.generator.sequence: An outputter bound together with OutputPattern and a generator.
BoundOutputter(OutputterChecked, OutputPattern, Generator<T>) - Constructor for class org.anchoranalysis.io.generator.sequence.BoundOutputter
BoundPhysicalExtent - Class in org.anchoranalysis.mpp.bean.bound
BoundPhysicalExtent() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
BoundPhysicalExtent(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
BoundPhysicalExtent(BoundPhysicalExtent) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
BoundReplaceStrategy<T extends FeatureInput,S extends ReplaceStrategy<T>> - Class in org.anchoranalysis.feature.session.strategy.replace.bind: Attaches a replacement-strategy to a session lazily (i.e.
BoundReplaceStrategy(Function<CacheCreator, S>) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.bind.BoundReplaceStrategy
BoundsFromRange<T> - Class in org.anchoranalysis.core.index.bounded
BoundsFromRange(GetterFromIndex<T>, BoundedRangeIncomplete) - Constructor for class org.anchoranalysis.core.index.bounded.BoundsFromRange
BoundUnitless - Class in org.anchoranalysis.mpp.bean.bound
BoundUnitless() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless
BoundUnitless(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless
BoundUnitless(BoundUnitless) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless
box() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.Mark
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
box(FeatureInputPairMemo, Function<FeatureInputPairMemo, VoxelizedMarkMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark: How we create our scaled masks
box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.Overlay: A bounding-box around the overlay
box(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Is this other bounding-box FULLY contained within this bounding box?
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.Mark
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.PointList
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
boxCopyTo(BoundingBox, Voxels<T>, BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.Base
boxCopyTo(BoundingBox, Voxels<T>, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Copies a bounding-box area to another Voxels
boxFromBounds(Point3d, double, boolean, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.conic.BoundingBoxCalculator: Calculates a bounding box for a point with a scalar radius in all dimensions
boxFromBounds(Point3d, DoubleMatrix1D, boolean, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.conic.BoundingBoxCalculator: Calculates a bounding box for a point with varying radii in each dimension (that have already been resolved into a matrix)
boxIterator() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
boxList(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
boxList(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
boxList(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
BoxPlot<T> - Class in org.anchoranalysis.plot.index
BoxPlot(String, String[], GetForSeries<T, String>, GetForSeries<T, BoxAndWhiskerItem>, GetForSeries<T, Paint>) - Constructor for class org.anchoranalysis.plot.index.BoxPlot
BranchChannels - Class in org.anchoranalysis.plugin.io.bean.stack.writer: Uses different raster-writers depending on the number/type of channels.
BranchChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
BranchIfDebug<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Uses one input-manager normally, but a different one if in debug mode
BranchIfDebug() - Constructor for class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
BranchStack - Class in org.anchoranalysis.plugin.io.bean.stack.writer: Uses different raster-writers depending on whether it is always 2D (not a z-stack) or possibly 3D.
BranchStack() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
bridge(int, H) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
bridge(int, H) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithIndex
bridge(int, H) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithoutIndex
Bridge - Class in org.anchoranalysis.plugin.image.bean.object.match: Matches to another object, and then uses that object to bridge to another
Bridge() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Bridge
bridgeElement(int, S) - Method in interface org.anchoranalysis.core.index.BridgeElementWithIndex
BridgeElementWithIndex<S,D,E extends Exception> - Interface in org.anchoranalysis.core.index
buffer() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: The associated buffer for storing the voxels.
buffer(VoxelBuffer, Extent, Function<U, T>, Function<AbstractNativeImg<S, T>, S>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.Wrap
BufferedImageFactory - Class in org.anchoranalysis.image.core.stack.bufferedimage
BufferedImageOverlay - Class in org.anchoranalysis.image.core.stack.bufferedimage
bufferListForSlice(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
bufferRel(int) - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
bufferValueEqualTo(T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base: Checks if the current value from a buffer is equal to a constant value
bufferValueGreaterThan(T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base: Checks if the current value from a buffer is greater than a constant value
bv - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
byDimension(int) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
byDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
byDimension(AxisType) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
byDimension(AxisType) - Method in class org.anchoranalysis.spatial.point.Tuple3i
bySymbol() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput: Calculates a feature if only an symbol (ID/name) is known, which refers to another feature.
bySymbol() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
ByteRepresentationForChannel - Interface in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats: Creates or retrieves a byte representation of the voxels for a particular slice.
bytesForSlice(int) - Method in interface org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.ByteRepresentationForChannel: The byte-representation of the voxels for a particular slice.
bytesPerPixel - Variable in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
bytesPerPixel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
bytesPerPixel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
bytesPerPixel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat

C

cache(CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.cache.CachedSupplier: Creates a cached-version of a CheckedSupplier
cache(StoreSupplier<T>) - Static method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier: Memoizes (caches) the supplied object, and returning it with an identical interface
cache(CheckedProgressingSupplier<T, E>) - Static method in class org.anchoranalysis.core.progress.CachedProgressingSupplier: Creates a cached-version of a CheckedProgressingSupplier
cache(NamedStacksSupplier) - Static method in interface org.anchoranalysis.image.core.stack.NamedStacksSupplier
cache(SerializedObjectSupplier<T>) - Static method in interface org.anchoranalysis.io.manifest.finder.SerializedObjectSupplier
CACHE_NAME_FIRST - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
CACHE_NAME_MERGED - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
CACHE_NAME_SECOND - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
CacheAndReuseStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.replace: Reuse (without needing to invalidate) an existing session-input as stored in a least-recently used cache, otherwise create a new one.
CacheAndReuseStrategy(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.CacheAndReuseStrategy
CacheCreator - Interface in org.anchoranalysis.feature.calculate.cache
CacheCreatorSimple - Class in org.anchoranalysis.feature.session.cache.creator
CacheCreatorSimple(FeatureList<? extends FeatureInput>, SharedFeatureMulti, FeatureInitParams, Logger) - Constructor for class org.anchoranalysis.feature.session.cache.creator.CacheCreatorSimple
CachedProgressingSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.progress: Memoizes (caches) a call to CheckedProgressingSupplier
CachedSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.cache: Memoizes (caches) a CheckedSupplier
CachedSupplierBase<T> - Class in org.anchoranalysis.core.cache: Base class for functions that memoize (cache) a call to an interface
CachedSupplierBase() - Constructor for class org.anchoranalysis.core.cache.CachedSupplierBase
cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
cacheResettable(StoreSupplier<T>) - Static method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier: Memoizes (caches) the supplied object, and returning it with a CachedSupplier interface
cachesToAvoidInvalidating() - Method in class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
cachesToAvoidInvalidating() - Method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
cachesToAvoidInvalidating() - Method in interface org.anchoranalysis.feature.session.strategy.child.FindChildStrategy: If set, these particular-caches are exceptionall NOT invalidated during the typical invalidation operation on their parent.
CacheSupplier<T extends FeatureInput,E extends Exception> - Interface in org.anchoranalysis.feature.session.strategy.child
CacheTransferSource<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.child: An existing cache that can be used as a source for child-caches elsewhere
CacheTransferSource(CacheSupplier<T, OperationFailedException>, Set<ChildCacheName>) - Constructor for class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
CacheTransferSourceCollection - Class in org.anchoranalysis.feature.session.strategy.child
CacheTransferSourceCollection() - Constructor for class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
calc(double, double, double, boolean, boolean) - Static method in class org.anchoranalysis.plugin.operator.feature.score.GaussianScoreCalculator
calc(FeatureList<T>, SessionInput<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCalculator: Calculates a feature-list throwing an exception if there is an error
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
calc(SessionInput<T>, FeatureCalculation<U, T>, Function<ResolvedCalculation<U, T>, CalculateInputFromDelegateOption<S, T, U>>, Feature<S>, ChildCacheName, double) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption: Calculates a feature using a cached-calculation as delegate, and optional Params return value
calc(FeatureInputObjectCollection) - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
calc(FeatureInputObjectCollection) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.collection.NumberObjects
calc(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.AxisRatioEllipsoid
calc(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
calc(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipsoidicity
calc(ObjectMask) - Method in interface org.anchoranalysis.image.feature.evaluator.PayloadCalculator
calc(ObjectMask, boolean) - Static method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
calc(FeatureInputMarkCollection) - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
calc(FeatureInputMarkCollection) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.collection.NumberMarks
calc(MemoCollection, EnergySchemeWithSharedFeatures, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
calculate(int[]) - Method in class org.anchoranalysis.image.feature.bean.score.VoxelScore
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.image.bean.spatial.ScaleCalculator
calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
calculate(Feature<S>, FeatureCalculation<S, T>, ChildCacheName) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild: Calculates a feature in a child-cache using a new input created from a FeatureCalculation
calculate(Feature<S>, S, ChildCacheName) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild: Calculates a feature in a child-cache
calculate(Feature<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput: Calculates the result of a feature using this input
calculate(Feature<T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
calculate(Feature<T>, SessionInput<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCalculator: Calculate a feature with particular values
calculate(FeatureList<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput: Calculates the results of several features using this input
calculate(FeatureList<T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
calculate(ChildCacheName, S, Function<CalculationResolver<S>, ResolvedCalculation<U, S>>) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild: Calculates a FeatureCalculation in a child-cache
calculate(ResolvedCalculation<S, T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput: Calculates a resolved Feature-calculation
calculate(ResolvedCalculation<S, T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
calculate(SessionInput<FeatureInput>) - Method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculation
calculate(SessionInput<FeatureInputResults>) - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
calculate(SessionInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
calculate(SessionInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
calculate(SessionInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
calculate(SessionInput<FeatureInputObjectCollection>) - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.First
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Merged
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Minimum
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.RatioFirstToSecond
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Second
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.SubtractSecondFromFirst
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxNumberVoxels
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMagnitude
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityCenterSlice
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityMIP
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberContourVoxelsOnSlice
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberVoxelsOnSlice
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipticity
calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
calculate(SessionInput<FeatureInputMarkCollection>) - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureMark
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.MaxRatioRadii
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.MarkEllipseCircumEstimate
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.Volume
calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsCollection
calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsSingleMark
calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.NumberMarks
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZDistance
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.MinimumDistanceByDimension
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.MinFeatureAsIndividual
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxels
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxelsMask
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.BBoxRatio
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MaxSliceArea
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Size
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.Feature
calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Constant
calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Reference
calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Sum
calculate(SessionInput<T>) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.DataTypeMaxIntensity
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Maximum
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Mean
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Minimum
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.NormalizedRange
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
calculate(FeatureCalculation<S, T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput: Calculates a feature-calculation after resolving it against the main cache
calculate(FeatureCalculation<S, T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.Count
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
calculate(FeatureInputPairObjects) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
calculate(FeatureInputPairObjects, FeatureList<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
calculate(FeatureInputSingleObject) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
calculate(FeatureInputSingleObject, FeatureList<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle
calculate(T) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti: Performs one calculation throwing an exception if something goes wrong
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
calculate(T) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingle: Performs one calculation throwing an exception if something goes wrong
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleChangeInput
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleFromMulti
calculate(T) - Method in class org.anchoranalysis.feature.session.SequentialSession: Calculates one params for each feature.
calculate(T, ErrorReporter, boolean) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti: Performs one calculation, either calling FeatureCalculatorMulti.calculate(T) or FeatureCalculatorMulti.calculateSuppressErrors(T, org.anchoranalysis.core.log.error.ErrorReporter) depending on a flag
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
calculate(T, FeatureList<T>) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti: Performs one calculation on a sub-set of the feature list throwing an exception if something goes wrong
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.SequentialSession
calculateAcceptanceProb(Kernel<?>, Optional<T>, T, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.AccptProbCalculator
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
calculateBound(Point3d, RotationMatrix) - Method in class org.anchoranalysis.mpp.bean.bound.BoundCalculator
calculateBound(Point3d, RotationMatrix) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
calculateBound(Point3d, RotationMatrix) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
calculateCheckInitialized(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.Feature
calculateConnectedComponentID(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
calculateContext(MarkFactoryContext) - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
calculateCornerMax() - Method in class org.anchoranalysis.spatial.box.BoundingBox: The maximum (right-most) point inside the box.
calculateCornerMaxExclusive() - Method in class org.anchoranalysis.spatial.box.BoundingBox: The maximum (right-most) point just outside the box.
calculateCountNonZero() - Method in class org.anchoranalysis.math.histogram.Histogram
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToFirst
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMaxVolume
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMerged
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToSecond
calculateDensityRatio(double, double, int) - Method in class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
CalculateDeriveMarkCollectionInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
CalculateDeriveMarkCollectionInput() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
CalculateDeriveMarkInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
CalculateDeriveMarkInput() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
CalculateDeriveObjectInput - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
CalculateDeriveObjectInput(int) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
CalculateDeriveSingleMemoFromPair - Class in org.anchoranalysis.mpp.feature.bean.energy.element
CalculateDeriveSingleMemoFromPair(boolean) - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
CalculateDilation - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateDilationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateDilationMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
CalculateDilationMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
calculateEccentricity(double, double) - Static method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
CalculateEllipseLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipse
CalculateEllipseLeastSquares() - Constructor for class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
CalculateEllipsoidLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
CalculateErosion - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateErosionMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
CalculateErosionMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
CalculateErosionMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
calculateFeatureByIdentifier(String, SessionInput<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSymbolCalculator: Searches for a feature that matches a particular identifier
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputObjectCollection>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectCollection
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputSingleObject>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObject
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<T>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
calculateFeaturesForObjects(ObjectCollection, EnergyStack, CalculateFeaturesForObjects.LabelsForInput<T>) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
CalculateFeaturesForObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.feature.calculator
CalculateFeaturesForObjects(CombineObjectsForFeatures<T>, InitParamsWithEnergyStack, boolean, InputProcessContext<FeatureTableCalculator<T>>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
CalculateFeaturesForObjects.LabelsForInput<T extends FeatureInput> - Interface in org.anchoranalysis.plugin.image.task.feature.calculator
calculateForAxis(Dimensions, AxisType) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Extent
calculateForAxis(Dimensions, AxisType) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
calculateForAxis(Dimensions, AxisType) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
CalculateForChild<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache: Performs calculations using child-caches instead of the main cache
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.DotProductOrientationToVector
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidAxisRatio
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidMaxAreaIntersectingPlane
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
calculateForNewMark(VoxelizedMarksWithEnergy, Set, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
calculateForNewMark(MarksFromPartition, Set, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
calculateForNewMark(T, Set, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShell
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellMaxSlice
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Area
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Volume
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase: Calculates the result for the specific moment identified by index
CalculateHistogram - Class in org.anchoranalysis.plugin.image.feature.stack.calculation
CalculateHistogram(int) - Constructor for class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
CalculateHistogramMasked - Class in org.anchoranalysis.plugin.image.feature.stack.calculation: Calculated a histogram for a specific region on a channel, as identified by a mask in another channel
CalculateHistogramMasked(int, int) - Constructor for class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
CalculateIncrementalOperationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
CalculateIncrementalOperationMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
CalculateIncrementalOperationMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
CalculateInputFromDelegate<S,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate: A base class for Cached-Calculations that generate a Params for feature-calculation using an existing "delegate" calculation
CalculateInputFromDelegate(ResolvedCalculation<U, T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
CalculateInputFromDelegate(FeatureCalculation<U, T>, CalculationResolver<T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
CalculateInputFromDelegateOption<S extends FeatureInput,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate: Like CalculateInputFromDelegate except assumes optional return value and no parameters
CalculateInputFromDelegateOption(ResolvedCalculation<U, T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption: The constructor
CalculateInputFromPair - Class in org.anchoranalysis.image.feature.object.calculation: Calculates a single-input from a pair
CalculateInputFromPair(CalculateInputFromPair.Extract) - Constructor for class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
CalculateInputFromPair.Extract - Enum in org.anchoranalysis.image.feature.object.calculation
CalculateIntersecting - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
CalculateIntersecting(ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>, int) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
calculateLevel(Histogram) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel: Determines a voxel intensity that can be used for thresholding.
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
CalculateLevel - Class in org.anchoranalysis.image.bean.threshold: Calculates a threshold-level from a histogram.
CalculateLevel - Class in org.anchoranalysis.plugin.image.feature.bean.score
CalculateLevel() - Constructor for class org.anchoranalysis.image.bean.threshold.CalculateLevel
CalculateLevel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
CalculateLevelBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
CalculateLevelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
calculateLevelIncoming(Histogram) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
CalculateLevelListBase - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
CalculateLevelListBase() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
CalculateLevelOne - Class in org.anchoranalysis.image.bean.threshold
CalculateLevelOne() - Constructor for class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
CalculateLevelRelativeToThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
CalculateLevelRelativeToThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
calculateMaximum() - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the maximum of the histogram values i.e.
calculateMaybeSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
calculateMeanIntensityObject(Channel, ObjectMask) - Static method in class org.anchoranalysis.plugin.image.intensity.IntensityMeanCalculator
calculateMeanIntensityObject(Channel, ObjectMask, boolean) - Static method in class org.anchoranalysis.plugin.image.intensity.IntensityMeanCalculator
calculateMemoryUsage() - Static method in class org.anchoranalysis.core.system.MemoryUtilities
calculateMinimum() - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the minimum of the histogram values i.e.
calculateMinMax(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds
calculateMode() - Method in class org.anchoranalysis.math.histogram.Histogram
calculateMode(int) - Method in class org.anchoranalysis.math.histogram.Histogram: Calculates the mode of the histogram values i.e.
calculateNewMaxCurrentValue() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
CalculateNumVoxels - Class in org.anchoranalysis.image.feature.object.calculation
CalculateNumVoxels(boolean) - Constructor for class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
CalculateObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
CalculateObjectMask(int, ResolvedCalculationMap<ObjectMask, FeatureInputSingleObject, Integer>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
CalculateObjectMask(CalculateObjectMask) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask: Copy constructor
CalculateOverlap - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlap(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
CalculateOverlapMask - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMask(int, int, byte) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
CalculateOverlapMIP - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMIP(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
CalculateOverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMIPBase(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
CalculateOverlapMIPRatio - Class in org.anchoranalysis.plugin.mpp.feature.overlap
CalculateOverlapMIPRatio(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
calculateOverlapRatio(ObjectMask, ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.OverlapCalculator
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
calculatePath() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
calculatePath() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
CalculatePointsFromOutline - Class in org.anchoranalysis.plugin.points.calculate
CalculatePointsFromOutline() - Constructor for class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
calculateResultsForInput(ProvidesStackInput, InputProcessContext<FeatureList<FeatureInputStack>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
calculateResultsForInput(FileInput, InputProcessContext<FeatureList<FeatureInputHistogram>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
calculateResultsForInput(T, InputProcessContext<FeatureList<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
calculateRunningSum(Mask, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.core.mask.IterateVoxelsMask: Calculates the sum and count across voxels intensity that correspond to on voxels on a mask
CalculateShellObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
CalculateShellObjectMask(ResolvedCalculation<ObjectMask, FeatureInputSingleObject>, ResolvedCalculation<ObjectMask, FeatureInputSingleObject>, int, boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
calculateSigma(Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.image.feature.histogram.Mean
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.CoefficientOfVariation
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Kurtosis
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Max
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Median
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Min
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Mode
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.NumberDistinctValues
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Skewness
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.StdDev
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Sum
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.TotalCount
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Variance
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
calculateSum() - Method in class org.anchoranalysis.math.histogram.Histogram
calculateSumCubes() - Method in class org.anchoranalysis.math.histogram.Histogram
calculateSumSquares() - Method in class org.anchoranalysis.math.histogram.Histogram
calculateSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
calculateSuppressErrors(FeatureInputSingleObject, ErrorReporter) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle
calculateSuppressErrors(T, ErrorReporter) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti: Performs one calculation recording the error to an ErrorReporter if anything goes wrong, but throwing no exception
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
calculateSuppressErrors(T, ErrorReporter) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingle: Performs one calculation recording the error to an ErrorReporter if anything goes wrong, but throwing no exception
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleChangeInput
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleFromMulti
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.SequentialSession: Calculates the next-object in our sequential series, reporting any exceptions into a reporter log
calculateTemperature(int) - Method in class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
calculateTemperature(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
calculateTemperature(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.NoAnnealing
calculateVolume() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
calculateVolume() - Method in class org.anchoranalysis.spatial.Extent
calculateVolumeAsInt() - Method in class org.anchoranalysis.spatial.Extent
calculateWith(Feature<T>, T, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession: Starts a feature-session for a single feature - and performs a calculation
calculateWithChannel(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
calculateWithChannel(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.HasTouchingVoxels
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxelFaces
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxels
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
calculateWithParameters(ObjectMask, OutlineKernelParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
calculateWithParameters(ObjectMask, OutlineKernelParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
calculateWithParameters(ObjectMask, OutlineKernelParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
calculateZScore(double, double, double) - Static method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
CalculationResolver<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache: Searches a cache to reuses a FeatureCalculation if it already exists.
calculator() - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache: A means of calculating feature values using this cache.
calculator() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
calculator() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
calculatorForAll(FeatureList<T>) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider: Calculates all image-features in the feature-store
calculatorSingleFromProvider(FeatureListProvider<T>, String) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider: Calculates a single-feature that comes from a provider (but can reference the other features from the store)
call() - Method in class org.anchoranalysis.experiment.task.processor.CallableJob
call(CheckedSupplier<T, E>) - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
CallableJob<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.task.processor: A job derived from a Task that can be placed on different threads
CallableJob(Task<T, S>, ParametersUnbound<T, S>, JobState, JobDescription, ConcurrentJobMonitor, Optional<MessageLogger>, int) - Constructor for class org.anchoranalysis.experiment.task.processor.CallableJob: Constructor
callChannelIfSupported(int, BiConsumer<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>>, Consumer<Channel>) - Method in class org.anchoranalysis.image.core.stack.ChannelMapper
callEachPointInNeighborhood(Point3i, Neighborhood, boolean, ProcessVoxelNeighbor<T>, int, int) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.IterateVoxelsNeighbors: Iterate over each point in the neighborhood of an existing point.
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.path.RootPath
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
canEqual(Object) - Method in class org.anchoranalysis.core.concurrency.WithPriority
canEqual(Object) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
canEqual(Object) - Method in class org.anchoranalysis.core.index.Indexable
canEqual(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputNull
canEqual(Object) - Method in class org.anchoranalysis.feature.io.name.SimpleName
canEqual(Object) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
canEqual(Object) - Method in class org.anchoranalysis.image.feature.stack.FeatureInputStack
canEqual(Object) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
canEqual(Object) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
canEqual(Object) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
canEqual(Object) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
canEqual(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
canEqual(Object) - Method in class org.anchoranalysis.overlay.IndexableOverlays
canEqual(Object) - Method in class org.anchoranalysis.plot.AxisLimits
canEqual(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
canEqual(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
canEqual(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
canEqual(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
canEqual(Object) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
canEqual(Object) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
canEqual(Object) - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
canEqual(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
canEqual(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3d
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3f
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3i
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3d
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3f
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3i
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Vector3d
canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
capacity() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: The capacity of the buffer ala Buffer.capacity.
capacity() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: The capacity (i.e.
castTo() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper: Casts voxels to a particular type
Cell - Class in org.anchoranalysis.image.bean.spatial.arrange
Cell() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Cell
centerOfGravity() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Calculates center-of-gravity across all axes
centerOfGravity() - Method in class org.anchoranalysis.spatial.box.BoundingBox: Similar to BoundingBox.midpoint() but not always identical.
centerOfGravity(AxisType) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Calculates center-of-gravity for one specific axis only
CenterOfGravity - Class in org.anchoranalysis.image.feature.bean.object.single
CenterOfGravity() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
CenterOfGravity(AxisType) - Constructor for class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity: Creates for a specific axis.
CenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
CenterOnMask() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
centerPoint() - Method in class org.anchoranalysis.mpp.mark.Mark
centerPoint() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.PointList
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
centerPoint() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
CenterSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
CenterSlice() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
CenterSliceBase - Class in org.anchoranalysis.plugin.mpp.bean.region
CenterSliceBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
CenterSliceWindow - Class in org.anchoranalysis.plugin.mpp.bean.region: Like {#link org.anchoranalysis.plugin.mpp.bean.region.CenterSlice} but considers more than one slice, specifically centerSlice+- windowSize
CenterSliceWindow() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
chainCode(int, int, int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
chainCodes(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding: Decodes a chain-code into a point
ChainCodesDirection - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Maps directions to chain codes
CHANGE_EXISTING_CHANNEL - org.anchoranalysis.image.core.channel.convert.ConversionPolicy
ChangeableOutputSequence<T,S> - Class in org.anchoranalysis.plugin.image.task.bean.format
ChangeableOutputSequence() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
changedMarkIDArray() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel: The mark ids that were changed in the last energy calculation for the kernel
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
changedOffset(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
changeExtent(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
changeExtentZ(int) - Method in class org.anchoranalysis.spatial.box.BoundingBox
changeInput(U) - Method in class org.anchoranalysis.experiment.task.InputBound: Immutably changes the input-object
changeIntensity(Voxels<?>, IntUnaryOperator) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Changes each voxel, reading and writing the buffer as an int.
changePrefix(DirectoryWithPrefix) - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: Creates a new OutputterTarget with a changed prefix.
changePrefix(DirectoryWithPrefix, Optional<WriteOperationRecorder>) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates a OutputterChecked with a changed prefix and WriteOperationRecorder.
changeZ(int, int) - Method in class org.anchoranalysis.spatial.box.BoundingBox
channel() - Method in class org.anchoranalysis.image.core.mask.Mask: The underlying channel which contains the binary-values.
channel(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
Channel - Class in org.anchoranalysis.image.core.channel: A channel from an image.
Channel(Voxels<?>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.channel.Channel: Constructor
channelAt(int) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
ChannelConverter<T> - Class in org.anchoranalysis.image.core.channel.convert: Converts a channel from one type to another specific type.
ChannelConverter(VoxelDataType, VoxelsConverter<T>, VoxelsFactoryTypeBound<T>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ChannelConverter
ChannelConverterAttached<S,T> - Interface in org.anchoranalysis.image.core.channel.convert.attached: A channel-converter that has been permanently attached to a particular object.
ChannelConverterMulti - Class in org.anchoranalysis.image.core.channel.convert: Converts a channel from one type to multiple other types.
ChannelConverterMulti() - Constructor for class org.anchoranalysis.image.core.channel.convert.ChannelConverterMulti
ChannelConvertStyle - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Converts a channel(s) at a particular timepoint into a stack(s).
ChannelConvertStyle() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ChannelConvertStyle
ChannelFactory - Class in org.anchoranalysis.image.core.channel.factory: Creates a channel for one of several data-types
ChannelFactoryByte - Class in org.anchoranalysis.image.core.channel.factory
ChannelFactoryByte() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryByte
ChannelFactoryFloat - Class in org.anchoranalysis.image.core.channel.factory
ChannelFactoryFloat() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryFloat
ChannelFactoryInt - Class in org.anchoranalysis.image.core.channel.factory
ChannelFactoryInt() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryInt
ChannelFactoryShort - Class in org.anchoranalysis.image.core.channel.factory
ChannelFactoryShort() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryShort
ChannelFactorySingleType - Class in org.anchoranalysis.image.core.channel.factory: Creates a channel for a specific data-type
ChannelFactorySingleType(VoxelDataType, VoxelsFactoryTypeBound<?>) - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
ChannelGetterForTimepoint - Class in org.anchoranalysis.plugin.image.task.channel
ChannelGetterForTimepoint(ChannelGetter, int) - Constructor for class org.anchoranalysis.plugin.image.task.channel.ChannelGetterForTimepoint
ChannelMapper - Class in org.anchoranalysis.image.core.stack: Helps a retrieve channel and an associated converter and apply operation on them jointly
ChannelMapper(IntFunction<Channel>, IntFunction<Optional<ChannelConverterAttached<Channel, UnsignedByteBuffer>>>) - Constructor for class org.anchoranalysis.image.core.stack.ChannelMapper
channelNames() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
channelNames() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
ChannelProvider - Class in org.anchoranalysis.image.bean.provider
ChannelProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProvider
ChannelProviderBinary - Class in org.anchoranalysis.image.bean.provider: A channel-provider based-on two input channel-providers that must be of the same dimensionality
ChannelProviderBinary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
ChannelProviderTernary - Class in org.anchoranalysis.image.bean.provider
ChannelProviderTernary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
ChannelProviderUnary - Class in org.anchoranalysis.image.bean.provider
ChannelProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
channels() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
ChannelSource - Class in org.anchoranalysis.plugin.image.task.grouped: Source of channels for aggregating.
ChannelSource(NamedStacks, ConsistentChannelChecker, Optional<SizeXY>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
check(Channel, String, Dimensions) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Checks a channel to make sure it's the same size as an an existing channel
check(Channel, Mask) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker
check(Mask, String, Dimensions) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Checks a channel to make sure it's the same size as an an existing channel
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.mpp.feature.bean.mark.CheckMark: Checks a mark
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AnySliceCenterOnMask
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.EllipseBoundsCheck
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
check(T) - Static method in class org.anchoranalysis.test.experiment.BeanTestChecker: Checks if a bean has all necessary items, throwing a run-time exception if it does not.
Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
Check() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
Check() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
checkAndInit(T, P, Logger) - Static method in class org.anchoranalysis.test.experiment.BeanTestChecker: Checks if a bean has all necessary items as with BeanTestChecker.check(T) and also initializes the bean.
CheckCacheForSpecificChildren - Class in org.anchoranalysis.feature.session.strategy.child: For particular child-caches, check if a session-input is available from another LRU-cache and reuse.
CheckCacheForSpecificChildren(Class<?>, CacheTransferSourceCollection) - Constructor for class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
checkChannelType(VoxelDataType) - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker: Checks that a channel has the same type (max value) as the others
checkCompatibleWith(Mark) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
CheckedBiConsumer<S,T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like BiConsumer but can also throw a checked exception.
CheckedBiFunction<S,T,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like BiFunction but can also throw a checked exception.
CheckedBooleanSupplier<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like BooleanSupplier but can also throw an exception.
CheckedConsumer<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Consumes a value and throws an exception
CheckedFunction<S,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like Function but can also thrown an exception.
CheckedIntConsumer<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Consumes an int and throws an exception
CheckedIntFunction<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like IntFunction but can also thrown an exception.
CheckedPredicate<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like Predicate but can also throw an exception.
CheckedProgressingSupplier<R,E extends Exception> - Interface in org.anchoranalysis.core.progress: Like CheckedSupplier but can update a progress-reporter as the operation progresses.
CheckedRunnable<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
CheckedStream - Class in org.anchoranalysis.core.functional: Map operations for streams that can throw checked-exceptions
CheckedStream.ConvertedToRuntimeException - Exception in org.anchoranalysis.core.functional: An exception that wraps another exception, but exposes itself as a RuntimeException
CheckedSupplier<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like Supplier but can also throw an exception.
CheckedToDoubleBiFunction<T,U,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like ToDoubleBiFunction but can also thrown an exception.
CheckedToIntFunction<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like ToIntFunction but can also thrown an exception.
CheckedUnaryOperator<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked: Like a UnaryOperator but allows an exception to be thrown
CheckException - Exception in org.anchoranalysis.mpp.feature.error
CheckException(String) - Constructor for exception org.anchoranalysis.mpp.feature.error.CheckException
CheckException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.feature.error.CheckException
CheckException(Throwable) - Constructor for exception org.anchoranalysis.mpp.feature.error.CheckException
checkExtentMatch(BoundingBox, BoundingBox) - Static method in class org.anchoranalysis.image.voxel.ExtentMatchHelper
CheckIfAllowed - Class in org.anchoranalysis.io.output.writer: Only allows outputs, if the output-name is allowed in the OutputterChecked.
CheckIfAllowed(SingleLevelOutputEnabled, Optional<WriterExecuteBeforeEveryOperation>, Writer) - Constructor for class org.anchoranalysis.io.output.writer.CheckIfAllowed
checkIfConnected() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Determines if an object-mask is connected.
CheckMark - Class in org.anchoranalysis.mpp.feature.bean.mark: A predicate on a mark to check if a condition has been satisfied.
CheckMark() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.CheckMark
CheckMarkWithMask - Class in org.anchoranalysis.plugin.mpp.bean.check
CheckMarkWithMask() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.bean.AnchorBean: Checks that a bean's properties conform to expectations.
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
checkMisconfigured(BeanInstanceMap) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
CheckMisconfigured - Class in org.anchoranalysis.bean.initializable: Routines for checking that particular patterns exist with bean-properties
CheckParsedFilePathBag - Class in org.anchoranalysis.plugin.io.bean.groupfiles.check
CheckParsedFilePathBag() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.check.CheckParsedFilePathBag
checkResultVector(ResultsVector) - Static method in class org.anchoranalysis.test.feature.ConstantsInListFixture: checks that a result-vector has the results we expect from the feature-list associated with this fixture
checkSize(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
checkUnsupported3D(Channel) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
checkUnsupportedObjectMask(Optional<ObjectMask>) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
checkUnsupportedSeeds(Optional<SeedCollection>) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache: Gets/creates a child-cache for a given name
childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in interface org.anchoranalysis.feature.session.strategy.child.FindChildStrategy: Selects a child-cache given a parent and a child-name
ChildCacheName - Class in org.anchoranalysis.feature.calculate.cache: A unique identifier for a child-cache name, that uses a class and optionally additionally a part-name a class: guaranteed to be unique for the class an optional part-name (string): a further division of the class into different caches
ChildCacheName(Class<?>) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName: Uses only the class as an identifier - and a blank part-name
ChildCacheName(Class<?>, int) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName: Uses only the class as an identifier - and a integer part-name
ChildCacheName(Class<?>, String) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName: Uses both the class and a part-name as an identifier
children() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
ChooseOneList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
ChooseOneList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ChooseOneList
Circle - Class in org.anchoranalysis.mpp.mark.conic: A circle
Circle() - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle
Circle(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle: Creates with a radius within particular bounds.
Circle(Circle) - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle: Copy constructor
circleAt(Point2i, double) - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture
CircleObjectFixture - Class in org.anchoranalysis.test.feature.plugins.objects
circumference(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
classificationString(boolean) - Static method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
classInCurrentJar() - Method in class org.anchoranalysis.launcher.config.LauncherConfig: a class which we use to determine the base location for pathRelativeProperties
clean() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
clean() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
cleanUp() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
cleanUp(VoxelPartitionFactory<Histogram>) - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
cleanUp(VoxelPartitionFactory<T>) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
cleanUp(VoxelPartitionFactory<T>) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
cleanUp(VoxelPartitionFactory<T>) - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
clear() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
clear() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
clear() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Clears the buffer ala Buffer.clear().
clear() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
clear() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
clearBest() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
clearVisualizationState() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
clearVisualizationState() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
clearVisualizationState() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
clip(Point3d, Dimensions) - Static method in class org.anchoranalysis.mpp.points.PointClipper
clip(Point3i, Dimensions) - Static method in class org.anchoranalysis.mpp.points.PointClipper
ClipHistogramMax - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Clips the input-histogram to a certain maximum value, and then delegates the calculate-level.
ClipHistogramMax() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
clipTo(Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Makes sure an object fits inside an extent, removing any parts which do not.
clipTo(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
clipTo(T, Extent) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask: Ensures the element lies within a certain extent.
close() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
close() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
close() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
close() - Method in class org.anchoranalysis.core.progress.ProgressReporterMultiple
close() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
close() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
close() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Closes any open file-handles.
close() - Method in class org.anchoranalysis.feature.io.results.ResultsWriter
close() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
close() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
close() - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
close() - Method in class org.anchoranalysis.plugin.image.task.slice.SharedStateSelectedSlice
close() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
close(boolean) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
close(boolean) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
close(boolean) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
close(boolean) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
close(boolean) - Method in interface org.anchoranalysis.experiment.log.StatefulMessageLogger
close(boolean) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
close(ErrorReporter) - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
close(ErrorReporter) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
close(ErrorReporter) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
close(ErrorReporter) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
close(ErrorReporter) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
close(ErrorReporter) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
closeAnyOpenIO() - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
closeAnyOpenIO() - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
closestPointOnBorder(Point3d) - Method in class org.anchoranalysis.spatial.box.BoundingBox
CODE_MINIMA - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
CODE_PLATEAU - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
CODE_TEMPORARY - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
CODE_UNVISITED - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
CoefficientOfVarianceFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
CoefficientOfVarianceFromAll() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
coefficientOfVariation(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics
CoefficientOfVariation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
CoefficientOfVariation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.CoefficientOfVariation
CollapseFileName - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive: Takes a file-path of form somedir/somename.ext and converts to somedir.ext
CollapseFileName() - Constructor for class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
CollectionGenerator<T> - Class in org.anchoranalysis.io.generator.collection: Writes a collection of elements as a subdirectory with each element as a single file in the subdirectory.
CollectionGenerator(Generator<T>, String) - Constructor for class org.anchoranalysis.io.generator.collection.CollectionGenerator
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: Collects the result of the operation after processing neighbor pixels
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Collects the result of the operation after processing neighbor pixels
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: Collects the result of the operation after processing neighbor pixels
collectResult() - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
colorAxis(Axis) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
colorChart(JFreeChart) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
ColorConverterBase - Class in org.anchoranalysis.plugin.opencv.bean.stack.provider.color: Converts a RGB stack into another color space using OpenCV
ColorConverterBase() - Constructor for class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ColorConverterBase
ColoredBase - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Base class for providers that draw entities (an outline or filled) on a background
ColoredBase() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
ColoredBaseWithGenerator - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Like ColoredBase but uses a generator to determine the colors for the objects
ColoredBaseWithGenerator() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
ColoredMarks - Class in org.anchoranalysis.mpp.mark
ColoredMarks - Class in org.anchoranalysis.plugin.mpp.bean.stack.provider: Draws a colored representation (outline or filled) of an MarkCollection on a background
ColoredMarks() - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
ColoredMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
ColoredMarks(MarkCollection, ColorIndex, IdentifierGetter) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
ColoredMarks(MarkCollection, ColorList) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
ColoredMarks(Mark, RGBColor) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
ColoredMarksWithDisplayStack - Class in org.anchoranalysis.mpp.io.marks
ColoredMarksWithDisplayStack(MarksWithDisplayStack, ColorIndex, IdentifierGetter) - Constructor for class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
ColoredMarksWithDisplayStack(ColoredMarks, DisplayStack) - Constructor for class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
ColoredMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Draws a colored representation (outline or filled) of a ObjectMask on a background
ColoredMask() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
ColoredObjectCollection - Class in org.anchoranalysis.plugin.image.object: Associates a ColorList with a ObjectCollection
ColoredObjectCollection() - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Create with an empty collection.
ColoredObjectCollection(ObjectCollection, ColorList) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Create with an existing object and color list.
ColoredObjectCollection(ObjectMask, RGBColor) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: Create with a single object and color.
ColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Draws a colored representation (outline or filled) of an ObjectCollection on a background
ColoredObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: Creates colored-objects to be drawn
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
ColoredOverlayCollection - Class in org.anchoranalysis.overlay.collection
ColoredOverlayCollection() - Constructor for class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
ColoredOverlayCollection(OverlayCollection, ColorList) - Constructor for class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
colorFor(ObjectWithProperties, int) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: A color for a particular object
colorForEachIndex(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorScheme: Assigns a color to each index value from a list of size numberColors.
ColorIndex - Interface in org.anchoranalysis.core.color
ColorIndexModulo - Class in org.anchoranalysis.core.color
ColorIndexModulo(ColorIndex) - Constructor for class org.anchoranalysis.core.color.ColorIndexModulo
colorLegend(LegendTitle) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
ColorList - Class in org.anchoranalysis.core.color
ColorList() - Constructor for class org.anchoranalysis.core.color.ColorList
ColorList(Color...) - Constructor for class org.anchoranalysis.core.color.ColorList
ColorList(RGBColor) - Constructor for class org.anchoranalysis.core.color.ColorList
ColorList(RGBColor...) - Constructor for class org.anchoranalysis.core.color.ColorList
colorPlot(CategoryPlot) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
colorPlot(XYPlot) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
ColorPool - Class in org.anchoranalysis.annotation.io.assignment.generator
ColorPool(int, ColorScheme, ColorScheme, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.ColorPool
ColorProvider - Class in org.anchoranalysis.image.bean.provider: Provides a list of one or more colors
ColorProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ColorProvider
ColorScheme - Class in org.anchoranalysis.bean.shared.color.scheme: Creates a set of related colors.
ColorScheme() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorScheme
ColorSchemeUnary - Class in org.anchoranalysis.bean.shared.color.scheme: Like ColorScheme but employs a unary operator on a call to an existing ColorScheme.
ColorSchemeUnary() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
ColorSchemeUnary(ColorScheme) - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ColorConverterBase: The color space conversion code to use from OpenCV
colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToHSV
colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToLab
column(int) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
ColumnDefinition - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
ColumnDefinition() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelAnd
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelOr
combine(Path, Path) - Static method in class org.anchoranalysis.bean.xml.factory.BeanPathUtilities
Combine - Class in org.anchoranalysis.plugin.io.bean.provider.file
Combine() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.Combine
CombineBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
CombineBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
CombineCSV - Class in org.anchoranalysis.plugin.io.bean.task
CombineCSV() - Constructor for class org.anchoranalysis.plugin.io.bean.task.CombineCSV
combined() - Method in class org.anchoranalysis.core.system.path.PathDifference: The directory-component (if it exists) and filename-component combined.
combined() - Method in class org.anchoranalysis.core.system.path.SplitPath
CombinedListGenerator<T> - Class in org.anchoranalysis.io.generator.combined: Several generators combined together with a common element-type.
CombinedListGenerator(Stream<NameValue<Generator<T>>>) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator
CombinedListGenerator(NameValue<Generator<T>>) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator
CombinedListGenerator(Generator<T>...) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator
CombinedName - Class in org.anchoranalysis.feature.io.name: A name which is unique when a primaryName is combined with a secondaryName
CombinedName(String, String) - Constructor for class org.anchoranalysis.feature.io.name.CombinedName: Creates with explicit strings for both parts.
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
combineDscrsRecursively(String, String) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Traverses through a set of nested-exceptions creating a description for each "combined" exception, and combining them into a single string.
CombineObjectsForFeatures<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine: A way to combine (or not combine) objects so that they provide a feature-table.
CombineObjectsForFeatures() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
combineToOnePath() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels: Combines all the contiguous paths to a single-path
combineToOnePath(List<ContiguousVoxelPath>) - Static method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.CombineToOnePath: Combines all the contiguous paths to a single-path
CombineToOnePath - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine
combineTypes(VoxelDataType, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.datatype.CombineTypes
CombineTypes - Class in org.anchoranalysis.image.voxel.datatype
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
CommandLineException - Exception in org.anchoranalysis.launcher: An exception thrown at run-time while processing command-line args
CommandLineException(String) - Constructor for exception org.anchoranalysis.launcher.CommandLineException
CommandLineExtracter - Class in org.anchoranalysis.launcher.options: Adds methods to CommandLine for querying and extracting options, with and without arguments.
CommandLineExtracter(CommandLine) - Constructor for class org.anchoranalysis.launcher.options.CommandLineExtracter
CommandLineOptions - Class in org.anchoranalysis.launcher.options: All command-line options used by the launcher.
common() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Creates a CommonContext a context that contains a subset of this context.
CommonContext - Class in org.anchoranalysis.core.log: A logger with additional configuration that are coupled together widely in the code
CommonContext(Logger, Path) - Constructor for class org.anchoranalysis.core.log.CommonContext
commonType(Stream<VoxelDataType>) - Static method in class org.anchoranalysis.image.voxel.datatype.FindCommonVoxelType: Finds a common type to represent (ideally without loss of precision} of a stream of types.
commonType(VoxelDataType, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.datatype.FindCommonVoxelType: Finds a common type to represent (ideally without loss of precision} both first and second.
Comparator3d<T extends Tuple3d> - Class in org.anchoranalysis.spatial.point
Comparator3d() - Constructor for class org.anchoranalysis.spatial.point.Comparator3d
Comparator3i<T extends Tuple3i> - Class in org.anchoranalysis.spatial.point
Comparator3i() - Constructor for class org.anchoranalysis.spatial.point.Comparator3i
ComparatorOrderByName<V> - Class in org.anchoranalysis.core.identifier.name: Orders two name-values by their name (alphabetic order from standard String.compareTo(String))
ComparatorOrderByName() - Constructor for class org.anchoranalysis.core.identifier.name.ComparatorOrderByName
compare(NameValue<V>, NameValue<V>) - Method in class org.anchoranalysis.core.identifier.name.ComparatorOrderByName
compare(T, T) - Method in class org.anchoranalysis.spatial.point.Comparator3d
compare(T, T) - Method in class org.anchoranalysis.spatial.point.Comparator3i
CompareAnnotations<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.bean.comparison: Task to compare a set of annotations to a segmentation or other set of annotations.
CompareAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
Comparer - Class in org.anchoranalysis.annotation.io.bean.comparer
Comparer() - Constructor for class org.anchoranalysis.annotation.io.bean.comparer.Comparer
compareTo(WithPriority<T>) - Method in class org.anchoranalysis.core.concurrency.WithPriority: Orders so that hasPriority==true has higher priority in queue to hasPriority==false
compareTo(IndexGetter) - Method in class org.anchoranalysis.core.index.Indexable
compareTo(MultiName) - Method in class org.anchoranalysis.feature.io.name.CombinedName
compareTo(MultiName) - Method in class org.anchoranalysis.feature.io.name.SimpleName
compareTo(EigenvalueAndVector) - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
compareTo(WithConfidence<T>) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
compareTo(SortedSetChannel) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
compareTo(SortedSetSlice) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
CompareWithRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Compares a value with a range, returning specified constants if its inside the range, below it or above it
CompareWithRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
CompareWithRangeFeature<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range.feature: Like CompareWithRange but uses features to calculate boundary values
CompareWithRangeFeature() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
CompatibleWithMark - Interface in org.anchoranalysis.mpp.mark
Compose<S,T,U> - Class in org.anchoranalysis.mpp.segment.transformer: Combines a transformation from S to U with one from U to T
Compose() - Constructor for class org.anchoranalysis.mpp.segment.transformer.Compose
Compose(StateTransformerBean<S, U>, StateTransformerBean<U, T>) - Constructor for class org.anchoranalysis.mpp.segment.transformer.Compose
CompressTIFF - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
CompressTIFF() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CompressTIFF
computeInitialFeasibleSolution() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Compute an initial feasible solution by assigning zero labels to the workers and by assigning to each job a label equal to the minimum cost among its incident edges.
Concatenate - Class in org.anchoranalysis.bean.define.adder: Concatenates a list of adders
Concatenate - Class in org.anchoranalysis.plugin.image.bean.color.provider
Concatenate - Class in org.anchoranalysis.plugin.image.bean.object.provider
Concatenate - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Combines all the channels from one or more sources (stacks, channels etc.)
Concatenate<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Concatenates several input-managers
Concatenate() - Constructor for class org.anchoranalysis.bean.define.adder.Concatenate
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
Concatenate() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Concatenate
ConcatenateFileTypes - Class in org.anchoranalysis.io.generator: Concatenates the arrays of FileType that may be returned from write operations.
ConcatenateFileTypes() - Constructor for class org.anchoranalysis.io.generator.ConcatenateFileTypes: Creates to always use a list for tracking.
ConcatenateFileTypes(boolean) - Constructor for class org.anchoranalysis.io.generator.ConcatenateFileTypes: Create to use a list for tracking if a flag is true, otherwise to just remember the last result of each call to ConcatenateFileTypes.add(org.anchoranalysis.io.manifest.file.FileType[]).
ConcurrencyPlan - Class in org.anchoranalysis.core.concurrency: How many allocated CPUS and CPUs can be used.
ConcurrentJobMonitor - Class in org.anchoranalysis.experiment.task.processor
ConcurrentJobMonitor(long) - Constructor for class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
ConcurrentModelException - Exception in org.anchoranalysis.core.concurrency: This exception indicates that an error occurred when performing inference from a model concurrently.
ConcurrentModelException(Throwable) - Constructor for exception org.anchoranalysis.core.concurrency.ConcurrentModelException
ConcurrentModelPool<T> - Class in org.anchoranalysis.core.concurrency: Keeps concurrent copies of a model to be used by different threads.
ConcurrentModelPool(ConcurrencyPlan, ConcurrentModelPool.CreateModelForPool<T>) - Constructor for class org.anchoranalysis.core.concurrency.ConcurrentModelPool
ConcurrentModelPool.CreateModelForPool<T> - Interface in org.anchoranalysis.core.concurrency: Creates a model to use in the pool
ConditionalKernel - Class in org.anchoranalysis.image.voxel.kernel
ConditionalKernel(BinaryKernel, int, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
ConditionallyMergeOverlappingObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce: Where objects overlap, they are merged together if certain conditions are fulfilled.
ConditionallyMergeOverlappingObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
ConfigureBioformatsLogging - Class in org.anchoranalysis.io.bioformats: Singleton class for making sure Bioformats is configured configured.
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
ConicBase - Class in org.anchoranalysis.mpp.mark.conic
ConicBase() - Constructor for class org.anchoranalysis.mpp.mark.conic.ConicBase
ConicBase(MarkWithPosition) - Constructor for class org.anchoranalysis.mpp.mark.conic.ConicBase
ConicFitterBase - Class in org.anchoranalysis.plugin.points.bean.fitter
ConicFitterBase() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
ConnectedComponentsFromBinarySegmentation - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Performs a binary-segmentation of the channel and converts its connected-components into objects
ConnectedComponentsFromBinarySegmentation() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
ConnectedComponentsFromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected: Converts a binary-mask into its connected components
ConnectedComponentsFromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
ConnectedComponentUnionFind - Class in org.anchoranalysis.image.voxel.object.factory.unionfind
ConnectedComponentUnionFind(int, boolean) - Constructor for class org.anchoranalysis.image.voxel.object.factory.unionfind.ConnectedComponentUnionFind
connectedTo(Contour) - Method in class org.anchoranalysis.spatial.Contour
connectedToFirstPointOf(Contour) - Method in class org.anchoranalysis.spatial.Contour
connectedToLastPointOf(Contour) - Method in class org.anchoranalysis.spatial.Contour
considerVisit(Point3i, int) - Method in interface org.anchoranalysis.image.core.outline.traverser.ConsiderVisit
considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
ConsiderVisit - Interface in org.anchoranalysis.image.core.outline.traverser
ConsistentChannelChecker - Class in org.anchoranalysis.plugin.image.task.grouped: Checks that the histograms created from channels all have the same data type, res, max-value etc.
ConsistentChannelChecker() - Constructor for class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker
ConsoleAccepted - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
ConsoleAccepted() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
ConsoleAggregatedReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
ConsoleAggregatedReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
ConsoleAggregatedReporter(double) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
ConsoleMessageLogger - Class in org.anchoranalysis.experiment.log
ConsoleMessageLogger() - Constructor for class org.anchoranalysis.experiment.log.ConsoleMessageLogger
Constant<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
Constant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: A constant value for thresholding
Constant - Class in org.anchoranalysis.plugin.io.bean.path.derive: Always generates a constant path irrespective of the the input
Constant - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
Constant() - Constructor for class org.anchoranalysis.feature.bean.operator.Constant
Constant() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
Constant() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Constant
Constant() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
Constant(double) - Constructor for class org.anchoranalysis.feature.bean.operator.Constant: Constructor with a particular value
Constant(int) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
Constant(String) - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Constant
Constant(String, double) - Constructor for class org.anchoranalysis.feature.bean.operator.Constant: Constructor with a particular value and a custom-name
ConstantBoundGenerator - Class in org.anchoranalysis.plugin.mpp.bean.bound
ConstantBoundGenerator() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
ConstantBoundGenerator(ResolvedBound) - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
ConstantsInListFixture - Class in org.anchoranalysis.test.feature
ConstantToThePowerOf<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
ConstantToThePowerOf() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
ConstantWeight - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight: All marks have weight of 1
ConstantWeight() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ConstantWeight
containerOptional() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
containerRequired() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
contains() - Method in class org.anchoranalysis.spatial.box.BoundingBox: For evaluating whether this bounding-box contains other points, boxes etc.?
contains(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
contains(int, int, int) - Method in class org.anchoranalysis.spatial.Extent
contains(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
contains(Object) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
contains(String) - Method in interface org.anchoranalysis.bean.StringBeanCollection
contains(String) - Method in class org.anchoranalysis.bean.StringList
contains(String) - Method in class org.anchoranalysis.bean.StringSet
contains(Feature<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
contains(ChildCacheName) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
contains(BoundingBox) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
contains(BoundingBox) - Method in class org.anchoranalysis.spatial.Extent
contains(Point2i) - Method in class org.anchoranalysis.spatial.Extent
contains(Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
contains(Point3d) - Method in class org.anchoranalysis.spatial.Extent
contains(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
contains(Point3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
contains(Point3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
contains(Point3i) - Method in class org.anchoranalysis.spatial.rtree.RTree: Which bounding-boxes contain a particular point.
contains(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
containsAll(Collection<?>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
containsChild(ChildCacheName) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
containsKey(Class<?>) - Method in class org.anchoranalysis.bean.BeanInstanceMap
containsKey(Object) - Method in class org.anchoranalysis.core.value.KeyValueParams
containsKey(String) - Method in class org.anchoranalysis.core.value.KeyValueParams
containsMark(Mark) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
containsVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Does the graph contain a particular vertex?
containsX(double) - Method in class org.anchoranalysis.spatial.Extent
containsX(int) - Method in class org.anchoranalysis.spatial.Extent
containsY(double) - Method in class org.anchoranalysis.spatial.Extent
containsY(int) - Method in class org.anchoranalysis.spatial.Extent
containsZ(double) - Method in class org.anchoranalysis.spatial.Extent
containsZ(int) - Method in class org.anchoranalysis.spatial.Extent
context() - Method in class org.anchoranalysis.experiment.task.InputBound
ContiguousVoxelPath - Class in org.anchoranalysis.image.core.outline.traverser.path: A list of visited pixels which forms one contiguous path (each voxel neighbors each other)
ContiguousVoxelPath() - Constructor for class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath: Without any connection-point
ContiguousVoxelPath(Point3i, Point3i) - Constructor for class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath: With a single initial-point, and maybe a connection point
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationCondition
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TriggerTerminationCondition
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
Contour - Class in org.anchoranalysis.spatial: A path of successively-neighbored points.
Contour() - Constructor for class org.anchoranalysis.spatial.Contour
ContourList - Class in org.anchoranalysis.plugin.points.contour
ContourList() - Constructor for class org.anchoranalysis.plugin.points.contour.ContourList
contoursForObject(ObjectMask) - Static method in class org.anchoranalysis.plugin.opencv.CVFindContours
ConversionPolicy - Enum in org.anchoranalysis.image.core.channel.convert
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ChannelConvertStyle: Converts a particular set of channels.
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
convert(Channel, ConversionPolicy) - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter
convert(Channel, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverterMulti
convert(Stack, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter
Convert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert: Converts a channel by applying a converter (no histogram is involved in the conversion).
Convert() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
convert2iTo3d(List<Point2i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
convert2iTo3f(List<Point2i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
convert3dTo3f(List<Point3d>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
convert3fTo3d(List<Point3f>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
convert3i(List<Point3d>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
convert3i(List<Point3f>, boolean) - Static method in class org.anchoranalysis.spatial.point.PointConverter
convert3iTo3f(List<Point3i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
ConvertBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
ConvertBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
ConvertChannelsInputToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack: An input object that converts NamedChannelsInput to StackSequenceInput
ConvertChannelsInputToStack(NamedChannelsInput) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
ConvertChannelsInputToStack(NamedChannelsInput, int, Optional<String>) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
ConvertChannelTo - Class in org.anchoranalysis.image.bean.channel.converter: Converts a channel from one type to another
ConvertChannelTo() - Constructor for class org.anchoranalysis.image.bean.channel.converter.ConvertChannelTo
ConvertChannelToWithHistogram - Class in org.anchoranalysis.image.bean.channel.converter
ConvertChannelToWithHistogram() - Constructor for class org.anchoranalysis.image.bean.channel.converter.ConvertChannelToWithHistogram
convertCode(int, int, EncodedVoxels, Point3i) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer: Convert code to connected-component
ConvertedToRuntimeException(Throwable) - Constructor for exception org.anchoranalysis.core.functional.CheckedStream.ConvertedToRuntimeException
convertFloat(FloatBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByType: Converts the current position in a FloatBuffer to the current position in a UnsignedShortBuffer.
convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType: Converts the current position in a FloatBuffer to the current position in a UnsignedShortBuffer.
convertFloat(FloatBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a FloatBuffer to the current position in a buffer of type T.
convertFrom(VoxelsWrapper, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Creates a new voxels of type T and copies the voxels from from.
ConvertFromImagePlus - Class in org.anchoranalysis.io.imagej.convert: Converts an ImagePlus into a channel or voxels.
ConvertFromMat - Class in org.anchoranalysis.plugin.opencv.convert
ConvertFromPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert: converts a feature to a physical distance in a XY place that is isometric
ConvertFromPhysicalVolume() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertFromPhysicalVolume
convertFromUnits(double, String) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits: Converts a value from another unit-type to base units.
convertFromUnits(double, SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits: Converts a value from another unit-type to base units.
ConvertImageFormat - Class in org.anchoranalysis.plugin.image.task.bean.format: Converts each input-image to the default output format, optionally changing the bit depth.
ConvertImageFormat() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
ConvertNamedChannels<T extends NamedChannelsInput,S,U extends NamedChannelsInput> - Class in org.anchoranalysis.plugin.mpp.experiment.bean: Converts NamedChannelsInput to a variety of others to match a delegate task
ConvertNamedChannels() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
ConvertNamedChannelsToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack: Manager that converts (one channel) NamedChannelsInput to StackSequenceInput
ConvertNamedChannelsToStack() - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
ConvertRGBToHSV - Class in org.anchoranalysis.plugin.opencv.bean.stack.provider.color
ConvertRGBToHSV() - Constructor for class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToHSV
ConvertRGBToLab - Class in org.anchoranalysis.plugin.opencv.bean.stack.provider.color
ConvertRGBToLab() - Constructor for class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToLab
convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: Converts a slice of single-channel into a newly created VoxelBuffer.
convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
ConvertTo<T> - Class in org.anchoranalysis.io.bioformats.copyconvert: Converts a subset of raw voxel bytes in a ByteBuffer to one or more destination channels.
ConvertTo(Function<VoxelsWrapper, Voxels<T>>) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo
convertTo3d(Point2d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
convertTo3i(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
convertTo3i(Point2i, int) - Static method in class org.anchoranalysis.spatial.point.PointConverter
ConvertToFactory - Class in org.anchoranalysis.io.bioformats.copyconvert
ConvertToImagePlus - Class in org.anchoranalysis.io.imagej.convert: Converts a channel or voxels into a ImagePlus.
ConvertToImageProcessor - Class in org.anchoranalysis.io.imagej.convert: Converts other voxel data-structures (as used by Anchor) to an ImageJ ImageProcessor.
ConvertToImg - Class in org.anchoranalysis.image.voxel.convert.imglib2: Converts the Voxels and VoxelBuffer data-types used in Anchor to the Img used in ImgLib2.
ConvertToMat - Class in org.anchoranalysis.plugin.opencv.convert: Converts common image data-structures used by Anchor to the Mat class used by OpenCV.
ConvertToNativeImg - Class in org.anchoranalysis.image.voxel.convert.imglib2: Converts the Voxels and VoxelBuffer data-types used in Anchor to the NativeImg used in ImgLib2.
convertToObjects(Dimensions) - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks: Creates an object-collection that is a voxelized representation of the marks in the annotation.
convertToOutputType(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertFromPhysicalVolume
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalAreaXY
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalVolume
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
ConvertToPhysicalAreaXY<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
ConvertToPhysicalAreaXY() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalAreaXY
ConvertToPhysicalDistance<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
ConvertToPhysicalDistance() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
ConvertToPhysicalDistance(Feature<T>, SpatialUnits.UnitSuffix, DirectionVector) - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
ConvertToPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert: converts a feature to a physical distance in a XY place that is isometric
ConvertToPhysicalVolume() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalVolume
convertToUnits(double, String) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits: Converts a value in base-units to another unit-type.
convertToUnits(double, SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits: Converts a value in base-units to another unit-type.
ConvertToVoxelBuffer - Class in org.anchoranalysis.io.imagej.convert: Converts a ImageProcessor to a voxel-buffer of particular data-type.
ConvertUnits<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.physical
ConvertUnits() - Constructor for class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
convertUnsignedByte(UnsignedByteBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertUnsignedByte(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByte
convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
convertUnsignedByte(UnsignedByteBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a UnsignedByteBuffer to the current position in a buffer of type T.
convertUnsignedInt(UnsignedIntBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByType
convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
convertUnsignedInt(UnsignedIntBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a UnsignedIntBuffer to the current position in a buffer of type T.
convertUnsignedShort(UnsignedShortBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByType
convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
convertUnsignedShort(UnsignedShortBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a UnsignedShortBuffer to the current position in a buffer of type T.
convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromSignedShort
convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromUnsignedShort
ConvertWithHistogram - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert: Converts a channel to a different voxel data-type by applying a converter with an associated histogram.
ConvertWithHistogram() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
convexHull2D(List<Point2i>) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities: Like ConvexHullUtilities.convexHull2D(List, int) but uses a default minimum number of points.
convexHull2D(List<Point2i>, int) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities: Apply a convex-hull algorithm to filter a set of points.
ConvexHull2D - Class in org.anchoranalysis.plugin.points.bean.mask.provider: Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
ConvexHull2D() - Constructor for class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull2D
ConvexHull3D - Class in org.anchoranalysis.plugin.points.bean.mask.provider
ConvexHull3D() - Constructor for class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull3D
ConvexHullBase - Class in org.anchoranalysis.plugin.points.bean.mask.provider
ConvexHullBase() - Constructor for class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
ConvexHullUtilities - Class in org.anchoranalysis.plugin.points.convexhull
copyAllChannels(Dimensions, ByteBuffer, DestinationChannelForIndex, int, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: Copies the channels in the source buffer into a particular DestinationChannelForIndex.
copyAllFrames(IFormatReader, List<Channel>, ProgressReporter, ImageFileShape, ConvertTo<?>, ReadOptions) - Static method in class org.anchoranalysis.io.bioformats.copyconvert.CopyConvert: Copies all frames, channels, z-slices (in a byte-array) into a destination set of Channels converting them if necessary along the way
copyBufferIndexTo(T, int, T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
copyChange(MarkCollection) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition: Makes a copy, with different marks
copyChangeIterationsDilation(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Copies the bean setting an new value for iterationsDilation
copyChangeParams(KeyValueParams) - Method in class org.anchoranalysis.feature.energy.EnergyStack
CopyConvert - Class in org.anchoranalysis.io.bioformats.copyconvert: Copies the bytes from a IFormatReader to a list of channels, converting if necessary.
CopyFilesExperiment - Class in org.anchoranalysis.plugin.io.bean.experiment
CopyFilesExperiment() - Constructor for class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
CopyFilesMethod - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
CopyFilesMethod() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CopyFilesMethod
CopyFilesNaming - Interface in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
CopyFilesNamingOne - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
CopyFilesNamingOne() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
CopyFilesNamingOneRegEx - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
CopyFilesNamingOneRegEx() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
copyFrom(int, int, ResultsVector, int) - Method in class org.anchoranalysis.feature.results.ResultsVector: Copies a contiguous subset of results from another vector
copyFrom(VoxelsWrapper, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source (of any type) to voxels of type T.
copyFromFloat(Voxels<FloatBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link FloatBuffer} to voxels of type T.
copyFromUnsignedByte(Voxels<UnsignedByteBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type T.
copyFromUnsignedInt(Voxels<UnsignedIntBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type T.
copyFromUnsignedShort(Voxels<UnsignedShortBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type T.
copyInit(Class<?>, NamedProviderStore<S>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine: Copies objects of a particular class from the define AND initializes
copyObjectsFrom(NamedProvider<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
copyPixelsTo(int, BoundingBox, Voxels<UnsignedByteBuffer>, BoundingBox) - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Copies pixels on a particular channel to an output buffer
copyProvider(Class<?>, NamedProviderStore<T>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine: Copies objects of a particular class from the define AND initializes as a provider
copyStackCollectionFrom(NamedProvider<Stack>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
copyTo(NameValueSet<Feature<T>>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
copyToDirectory(File) - Method in class org.anchoranalysis.test.TestLoader: Copies all the data in the test-data folder (recursively), preserving file-dates
copyToDirectory(String[], File) - Method in class org.anchoranalysis.test.TestLoader: Copies specific subdirectories from the test-data folder (recursively), preserving file-dates
copyToDuplicate(NameValueSet<Feature<T>>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
copyVoxelsTo(ObjectMask, VoxelsWrapper, BoundingBox) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
copyVoxelsTo(BoundingBox, VoxelsWrapper, BoundingBox) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
copyWithoutInit(Class<?>, NamedProviderStore<S>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine: Copies objects of a particular class from the define WITHOUT doing any initialization
cornerMin() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
cornerMin() - Method in class org.anchoranalysis.spatial.box.BoundingBox: The bottom-left corner of the bounding box.
CostMatrix<T> - Class in org.anchoranalysis.annotation.io.assignment: Stores costs between all possible pairings between elements from two lists.
CostOverlapWithinMidpointDistance - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: TODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheable
CostOverlapWithinMidpointDistance() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
count() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
count() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
count() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Counts the number of values satisfying the predicate - across all voxels.
Count - Class in org.anchoranalysis.feature.bean.results: The number of the results from a particular feature.
Count - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: Counts the number of items in a histogram (posssibly in relation to a threshold: above, below etc.)
Count() - Constructor for class org.anchoranalysis.feature.bean.results.Count
Count() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
countAtPosition(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernel
countAtPosition(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase: This method is deliberately not broken into smaller pieces to avoid inlining.
countByte(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingBounded: Counts all voxels in the intersection of two bounded-voxels of type BoundedVoxels that match a predicate.
countByteMasked(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingBounded: Counts all voxels intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask and match a predicate.
CountEqual - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
CountEqual() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
Counter - Class in org.anchoranalysis.math.arithmetic: A simple counter that increments
Counter() - Constructor for class org.anchoranalysis.math.arithmetic.Counter
countForObject(ObjectMask) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
countForObject(ObjectMask) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
countForObject(ObjectMask) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Counts the number of values satisfying the predicate - but restricted to voxels corresponding to on in an object-mask.
countIntersectingVoxels() - Method in class org.anchoranalysis.mpp.overlap.MaxIntensityProjectionPair
countIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
countIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Counts the number of intersecting-voxels between two object-masks.
countIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingObjects: Counts the number of intersecting-voxels between two object-masks.
CountKernel - Class in org.anchoranalysis.image.voxel.kernel.count
CountKernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernel
CountKernelNeighborhood - Class in org.anchoranalysis.image.voxel.kernel.count: For every voxel on the outline, count ALL neighbors that are adjacent, including those lying outside the scene.
CountKernelNeighborhood(boolean, BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhood
CountKernelNeighborhoodBase - Class in org.anchoranalysis.image.voxel.kernel.count: The number of touching-faces of a voxel with a neighbor
CountKernelNeighborhoodBase(boolean, BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
CountKernelNeighborhoodIgnoreOutsideScene - Class in org.anchoranalysis.image.voxel.kernel.count: For every voxel on the outline, count ALL neighbors that are adjacent, but ignoring any outside the scene.
CountKernelNeighborhoodIgnoreOutsideScene(boolean, BinaryValuesByte, boolean, Extent, ReadableTuple3i) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodIgnoreOutsideScene
CountKernelNeighborhoodMask - Class in org.anchoranalysis.image.voxel.kernel.count: The number of touching-faces of a voxel with a neighbor, so long as the neighbor is part of an object-mask
CountKernelNeighborhoodMask(boolean, BinaryValuesByte, ObjectMask, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask
countOff() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
countOn() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
countThreshold(RelationToThreshold) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
countThreshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
countThreshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
countThreshold(RelationToValue, double) - Method in class org.anchoranalysis.math.histogram.Histogram
CountVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like IterateVoxelsBoundingBox but counts voxels matching a predicate rather than iterating.
CountVoxelsIntersectingObjects - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like CountVoxelsIntersectingBounded but specifically counts areas of intersection between two ObjectMasks.
CoupledManifests - Class in org.anchoranalysis.plugin.io.manifest
CoupledManifests(Manifest, DeserializedManifest, Logger) - Constructor for class org.anchoranalysis.plugin.io.manifest.CoupledManifests
CoupledManifests(DeserializedManifest, int, Logger) - Constructor for class org.anchoranalysis.plugin.io.manifest.CoupledManifests
CoupledManifestsInputManager - Class in org.anchoranalysis.plugin.io.bean.input.manifest
CoupledManifestsInputManager() - Constructor for class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
create() - Method in interface org.anchoranalysis.bean.provider.Provider
create() - Method in class org.anchoranalysis.bean.provider.ProviderHolder
create() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProvider
create() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
create() - Method in class org.anchoranalysis.bean.shared.random.RandomNumberGeneratorBean
create() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
create() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
create() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
create() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
create() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
create() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
create() - Method in class org.anchoranalysis.bean.shared.StringMap
create() - Method in class org.anchoranalysis.feature.bean.list.Define
create() - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed
create() - Method in class org.anchoranalysis.feature.bean.list.DefineSingle
create() - Method in class org.anchoranalysis.feature.bean.list.FeatureListProvider
create() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
create() - Method in class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
create() - Method in class org.anchoranalysis.feature.bean.list.PrependName
create() - Method in class org.anchoranalysis.feature.bean.list.SelectFromShared
create() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProvider
create() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
create() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
create() - Method in class org.anchoranalysis.image.bean.interpolator.ImgLib2Lanczos
create() - Method in class org.anchoranalysis.image.bean.interpolator.ImgLib2Linear
create() - Method in class org.anchoranalysis.image.bean.interpolator.InterpolatorBean
create() - Method in class org.anchoranalysis.image.bean.interpolator.None
create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProvider
create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
create() - Method in class org.anchoranalysis.image.bean.provider.ColorProvider
create() - Method in class org.anchoranalysis.image.bean.provider.DimensionsProvider
create() - Method in class org.anchoranalysis.image.bean.provider.HistogramProvider
create() - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
create() - Method in class org.anchoranalysis.image.bean.provider.MaskProvider
create() - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
create() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProvider
create() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
create() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
create() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProvider
create() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkFactory
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkPointListFactory
create() - Method in class org.anchoranalysis.mpp.bean.provider.MarkBoundsProvider
create() - Method in class org.anchoranalysis.mpp.bean.provider.MarkCollectionProvider
create() - Method in class org.anchoranalysis.mpp.bean.provider.SingleMarkProvider
create() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreator
create() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
create() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
create() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
create() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
create() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.GuessDimensions
create() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
create() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Empty
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
create() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
create() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
create() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
create() - Method in interface org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder.CreateFirstSecondOrder
create() - Method in class org.anchoranalysis.plugin.imagej.bean.interpolator.InterpolatorBeanImageJ
create() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
create() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
create() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
create() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
create() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.CreateNew
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
create() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
create() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
create() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
create() - Method in class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory: Creates a RotationMatrix.
create() - Static method in class org.anchoranalysis.test.feature.ConstantsInListFixture: creates a feature-list associated with the fixture
create(boolean) - Method in interface org.anchoranalysis.core.concurrency.ConcurrentModelPool.CreateModelForPool: Creates a model
create(boolean, Supplier<T>) - Static method in class org.anchoranalysis.bean.OptionalFactory: Creates only if a boolean flag is true, otherwise returns empty.
create(int) - Method in class org.anchoranalysis.image.core.object.label.DecodeLabels: Creates a list of elements from voxels that are labelled with unique integers (sequentially increasing)
create(int) - Method in interface org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactory
create(int) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactoryHistogramReuse
create(int) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitonFactoryHistogram
create(BufferedImage) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.CreateStackFromBufferedImage
create(Class<? extends FeatureInput>) - Method in interface org.anchoranalysis.feature.calculate.cache.CacheCreator
create(Class<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.session.cache.creator.CacheCreatorSimple
create(String) - Static method in class org.anchoranalysis.bean.OptionalFactory: Creates Optional.empty() for an empty string, or otherwise Optional.of
create(String) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Creates an Optional from a string that might be empty or null
create(String, Optional<ManifestDescription>, OutputterChecked, String) - Static method in class org.anchoranalysis.io.generator.text.TextFileOutputter: Creates a TextFileOutput.
create(Path) - Static method in class org.anchoranalysis.io.generator.tabular.CSVWriter: Creates and starts a CSVWriter (it's always allowed, so will never return null)
create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.bean.Plot: Creates a graph
create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.LinePlot
create(List<Point3d>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
create(List<Point3d>, int) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
create(List<Point3i>) - Static method in class org.anchoranalysis.image.core.object.factory.SingleObjectFromPointsFactory
create(List<T>) - Method in interface org.anchoranalysis.bean.xml.factory.CreateFromList
create(List<T>, List<T>, boolean, CheckedToDoubleBiFunction<T, T, CreateException>) - Static method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: Creates by calculating the cost between elements.
create(List<V>, Function<V, ObjectMask>, Extent, boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborGraph: Create the graph with object-masks as vertices, where edges represent the number of intersecting voxels between objects.
create(Map<Integer, T>, UnaryOperator<T>) - Method in class org.anchoranalysis.image.core.object.label.DecodeLabels: Creates a map of elements to other elements that are labelled with unique integers (sequentially increasing) in voxels.
create(Optional<String>, String) - Static method in class org.anchoranalysis.feature.io.name.MultiNameFactory: Creates either a multi-name that is either has a single part or a double part.
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.AddToDefaults
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.NoneExcept
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnabledRules: Creates rules for determining whether an output is enabled or disabled.
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.Permissive
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.
create(IFormatReader, VoxelDataType, int) - Static method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertToFactory
create(Provider<T>) - Static method in class org.anchoranalysis.bean.OptionalFactory: Creates from a provider if non-null.
create(SharedObjects) - Static method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsInitParams
create(SharedObjects) - Static method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
create(Logger, Path) - Static method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams: Creates empty params
create(FeatureList<T>, SharedFeatureSet<T>) - Method in interface org.anchoranalysis.feature.session.cache.FeatureSessionCacheFactory
create(FeatureList<T>, SharedFeatureSet<T>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCacheFactory
create(FeatureList<T>, SharedFeatureSet<T>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCacheFactory
create(FeatureCSVMetadata, Outputter) - Static method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter: Maybe creates a FeatureCSVWriter depending if the output is allowed.
create(ImageInitParams, SharedObjects) - Static method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
create(Channel) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
create(Channel) - Static method in class org.anchoranalysis.image.core.stack.DisplayStack
create(Channel, Mask) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
create(Channel, ObjectCollection) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
create(Channel, ObjectMask) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
create(Dimensions, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory: Creates an empty initialized channel for a particular data-type
create(RGBStack) - Static method in class org.anchoranalysis.image.core.stack.DisplayStack
create(Stack) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageFactory
create(Stack) - Static method in class org.anchoranalysis.image.core.stack.DisplayStack
create(BinaryVoxels<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
create(VoxelBuffer<?>) - Static method in class org.anchoranalysis.image.voxel.statistics.HistogramFactory
create(SliceBufferIndex<T>) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
create(SliceBufferIndex<T>, VoxelDataType) - Method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
create(ObjectCollection, Extent, boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborGraph: Create the graph with object-masks as vertices, where edges represent the number of intersecting voxels between objects.
create(Voxels<?>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
create(Voxels<?>, Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
create(Voxels<?>, Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
create(VoxelsWrapper) - Static method in class org.anchoranalysis.image.voxel.statistics.HistogramFactory
create(VoxelsWrapper, Optional<ObjectMask>) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
create(InputManagerParams) - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
create(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Combine
create(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
create(InputManagerParams) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
create(InputOutputContext, Optional<Define>, Optional<? extends InputForMPPBean>) - Static method in class org.anchoranalysis.mpp.io.input.MPPInitParamsFactory
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination: Creates a logger for this destination
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToConsole
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFile
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileOnlyIfFailure
create(Mark) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
create(Mark, EnergyStackWithoutParams, RegionMap) - Static method in class org.anchoranalysis.mpp.mark.voxelized.memo.PxlMarkMemoFactory
create(Mark, EnergyStackWithoutParams, RegionMap) - Static method in class org.anchoranalysis.mpp.mark.voxelized.VoxelizedMarkFactory
create(Extent, VoxelDataType) - Method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
create(CommandLine, Path, Path, Path) - Static method in class org.anchoranalysis.launcher.executor.ExperimentExecutorFactory: Creates an experiment-executor from a command line that EITHER: uses a default-experiment OR accepts a path passed as the first command-line argument
createAddCriteria() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceFirstAndSecond
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceRatioFirstAndSecond
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.SubtractReducedFromMerged
createAndStartSession() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
createArguments(CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
createAscending() - Static method in class org.anchoranalysis.test.feature.plugins.HistogramFixture: a histogram from 0 to 255 (inclusive) where each bin is equal to its index (value 5 has count 5, value 100 has count 100 etc.)
createAssignment(ObjectCollection, ObjectCollection, double, Dimensions) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentObjectFactory
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
createAsStack() - Method in class org.anchoranalysis.image.bean.provider.ChannelProvider
createAsStack() - Method in class org.anchoranalysis.image.bean.provider.MaskProvider
createAsStack() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProvider
createAsStack() - Method in interface org.anchoranalysis.image.core.stack.ProviderAsStack: Creates from the image-bean in the form of a stack
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientXY
createBackground(NamedProviderStore<Stack>, String) - Static method in class org.anchoranalysis.mpp.io.output.BackgroundCreator
createBean(Class<?>, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.define.DefineFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.IncludeBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.IncludeListFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.IndirectlyFromListBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.ListBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.ReplacePropertyBeanFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.StringListFactory
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.StringSetFactory
createBeanInstance(Class<?>, BeanDeclaration) - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
createBetweenTwoPoints(Point3d, Point3d) - Static method in class org.anchoranalysis.image.core.orientation.DirectionVector
createBetweenTwoPoints(Point3i, Point3i) - Static method in class org.anchoranalysis.image.core.orientation.DirectionVector
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in interface org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStack
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Single
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
createBufferedImage() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
createBufferedImage(int, int) - Method in class org.anchoranalysis.plot.PlotInstance
createBufferedImageBBox(BoundingBox) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
createByte() - Method in class org.anchoranalysis.image.core.mask.Mask
createByte() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
createByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for UnsignedByteBuffer.
createByte(Voxels<UnsignedByteBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create voxels-assigner for UnsignedByteBuffer.
createByte(BoundingBox) - Static method in class org.anchoranalysis.image.voxel.BoundedVoxelsFactory
createByte(Extent, IntFunction<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create voxels-arithmethic for UnsignedByteBuffer
createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
createCalculator(CreateCalculatorHelper, ImageInitParams, BoundReplaceStrategy<FeatureInputStack, ? extends ReplaceStrategy<FeatureInputStack>>) - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
createChannel() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
createChannel(int, boolean) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
createChannelDuplicate(int) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
createChannelDuplicateForBoundingBox(int, BoundingBox) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
createChart(DefaultCategoryDataset, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.BarPlot: Creates a chart
createChart(DefaultBoxAndWhiskerCategoryDataset, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.BoxPlot
createChart(XYDataset, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.LinePlot: Creates a chart
createChart(S, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
createCollection(Channel, ObjectCollection, CalculateLevel, int, MessageLogger) - Static method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollectionFactory
createColor(ColoredMarks, RegionMembershipWithFlags) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
createColors(int) - Method in class org.anchoranalysis.annotation.io.assignment.generator.ColorPool
createCombinedContour() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
createCombinedException(String, Throwable) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
CreateCombinedStack - Class in org.anchoranalysis.image.bean.nonbean.init
createConnectedComponents(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
createConverter() - Method in class org.anchoranalysis.image.bean.channel.converter.ConvertChannelTo
createConverter() - Method in class org.anchoranalysis.image.bean.channel.converter.ConvertChannelToWithHistogram
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByTypeToByte
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByte
createCountKernelMask(ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
createDataset(Iterator<T>) - Method in class org.anchoranalysis.plot.index.LinePlot
createDataset(Iterator<T>) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
createDataset(Iterator<T>) - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical: Creates a sample dataset
createDefaultDataset() - Method in class org.anchoranalysis.plot.index.BarPlot
createDefaultDataset() - Method in class org.anchoranalysis.plot.index.BoxPlot
createDefaultDataset() - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
createDescending() - Static method in class org.anchoranalysis.test.feature.plugins.HistogramFixture
createDescriptor(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
createDesignMatrix(List<Point3f>) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
createDestinationFile(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CopyFilesMethod
createDilatedObject(ObjectMask, Optional<Extent>, boolean, int, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation: Dilates an object-mask, growing the bounding-box as necessary.
createDilationKernel(BinaryValuesByte, Optional<Voxels<UnsignedByteBuffer>>, int) - Method in class org.anchoranalysis.image.voxel.object.morphological.DilationKernelFactory
createDim() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
createDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
createDims() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase: Returns the dimensions or null if none are provided
createDistanceMapForMask(Mask, boolean, double, double, boolean, boolean) - Static method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>, boolean, double, double, boolean, boolean) - Static method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
createDocumentBuilder() - Static method in class org.anchoranalysis.bean.xml.XmlUtilities
createDuplicatePxlMarkMemoList() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
CreateEllipse - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
CreateEllipse() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
createEmptyInitialised(Dimensions) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
createEmptyInitialisedToSupportMaxValue(Dimensions, long) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory: Creates an empty initialized channel with discrete type with as minimal as needed data-type to support a maximum value
createEmptyMat(Extent, int) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
createEmptyOff(Extent) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off (0).
createEmptyOff(Extent, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Creates an empty binary-voxels of a particular data-type with all voxels initialized to OFF (0)
createEmptyOn(Extent) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to ON (255)
createEmptyUninitialised(Dimensions) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
createEnergyStack(ImageInitParams, Logger) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
createErodedObject(ObjectMask, Optional<Extent>, boolean, int, boolean, Optional<AcceptIterationConditon>) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion
CreateException - Exception in org.anchoranalysis.core.exception
CreateException(String) - Constructor for exception org.anchoranalysis.core.exception.CreateException
CreateException(String, AnchorCombinableException) - Constructor for exception org.anchoranalysis.core.exception.CreateException
CreateException(String, HasFriendlyErrorMessage) - Constructor for exception org.anchoranalysis.core.exception.CreateException
CreateException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.CreateException
createExperimentExecutor(CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
createExperimentOutputter(String, Manifest, RecordedOutputsWithRules, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Creates an outputter for the experiment in general.
createExperimentState() - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
createExperimentState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueIndividualEnergyGreaterThan
createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueMarkGreaterEqualThan
CreateFeatureInput<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session
createFeatureList(String, TestLoader) - Static method in class org.anchoranalysis.test.feature.plugins.FeaturesFromXmlFixture
createFeatureNames() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
createFeatureNames() - Method in interface org.anchoranalysis.image.feature.session.FeatureTableCalculator: Creates A list of names for each feature (columns of the table)
createFeatureNames() - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
createFeatureNames() - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Creates features that will be applied on the objects.
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
createFeatures(NamedFeatureStore<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
createFeatureSession() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Creates session for evaluating feature optionally adding an energy-stack.
createFeatureSession(UnaryOperator<FeatureList<T>>, SharedObjects) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator: Creates session for evaluating features.
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in interface org.anchoranalysis.io.output.writer.Writer: The path to write a particular output to.
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: The path to write a particular output to.
createFileOutputFor(String, FeedbackBeginParameters<VoxelizedMarksWithEnergy>, String) - Static method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterUtilities
createFitResultFromMatrixAandCenter(DoubleMatrix2D, DoubleMatrix2D, boolean) - Static method in class org.anchoranalysis.plugin.points.bean.fitter.EllipsoidFitHelper
createFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for FloatBuffer
createFloat(Voxels<FloatBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create voxels-assigner for FloatBuffer.
createFloat(Extent, IntFunction<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create voxels-arithmethic for FloatBuffer
createForBuffer(VoxelBuffer<T>, Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
createForDirectoryPermissive(Path, boolean) - Static method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates, defaulting to a permissive output-manager in a a particular directory.
createForFeature(Feature<?>) - Method in interface org.anchoranalysis.feature.session.CreateFeatureInput
createForFeatures(List<NamedBean<FeatureListProvider<T>>>, LabelHeaders, ResultsWriterOutputNames, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures: Alternative static constructor that creates a shared-state from a list of named feature-providers
createForFeatures(ResultsWriterOutputNames, FeatureTableCalculator<T>, LabelHeaders, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures: Alternative static constructor that creates a shared-state from a feature-store
createForFeatures(NamedFeatureStore<T>, LabelHeaders, ResultsWriterOutputNames, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures: Alternative static constructor that creates a shared-state from a feature-store
createForSingle(AnchorBean<?>, String) - Static method in class org.anchoranalysis.bean.permute.setter.PermutationSetterUtilities: Searches through a list of property fields to find one that matches the propertyName
createForSubdirectory(String) - Method in class org.anchoranalysis.test.TestLoader: Creates a new test-loader for a subdirectory of the current test
createFrom(int, ObjectMask) - Method in interface org.anchoranalysis.image.core.object.label.DecodeLabels.CreateElementFromScaledObject
createFrom(int, ObjectMask) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask: Creates an element of type T from an object-representation and index.
createFrom3Vecs(DoubleMatrix1D, DoubleMatrix1D, DoubleMatrix1D) - Static method in class org.anchoranalysis.spatial.rotation.RotationMatrix
createFromChannel(Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.MinimumFilter
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.Invert
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Duplicate
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.Sobel
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractCenterSlice
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MaximumIntensityProjection
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MeanIntensityProjection
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.EdgeFilterIJ
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter3D
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.MeanFilter2D
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.VarianceFilter2D
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter2D
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeObjectIntensity
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.IdentifyObjects
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOff
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOn
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
createFromExistingCollections(InputOutputContext, Optional<Define>, Optional<NamedProvider<Stack>>, Optional<NamedProvider<ObjectCollection>>, Optional<KeyValueParams>) - Static method in class org.anchoranalysis.mpp.io.input.MPPInitParamsFactory
createFromExplicitDirectory(String) - Static method in class org.anchoranalysis.test.TestLoader: Creates a new test-data loader using an explicit File path as root
createFromExplicitDirectory(Path) - Static method in class org.anchoranalysis.test.TestLoader: Creates a new test-data loader using an explicit File path as root
createFromFile(Path) - Method in class org.anchoranalysis.io.manifest.directory.sequenced.DeriveElementsFromSequencedDirectory: Creates an element of type T from a one particular file in the sequence.
createFromFile(Path) - Method in class org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectoryDeserializer
createFromFlag(boolean, Supplier<T>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Creates an Optional from a boolean flag
createFromFlag(boolean, T) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Creates an Optional from a boolean flag
createFromFlagChecked(boolean, CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Creates an Optional from a boolean flag - where the supplier can thrown an exception
createFromFlagOptional(boolean, Supplier<Optional<T>>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Creates an Optional from a boolean flag and a supplier that returns an Optional
createFromHistogram(Histogram) - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
createFromHistogram(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
createFromHistogram(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
createFromList(List<T>, Function<T, BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundedList: Creates for a list, minimally fitting a bounding-box around all elements
CreateFromList<T> - Interface in org.anchoranalysis.bean.xml.factory
createFromMarks(MarkCollection, KernelCalculationContext, Logger) - Static method in class org.anchoranalysis.plugin.mpp.segment.optimization.VoxelizedMarksWithEnergyFactory
createFromMask(Mask) - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMask
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Duplicate
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.FlattenZ
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull2D
createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull3D
createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.ZeroOutsideMask
createFromMavenWorkingDirectory() - Static method in class org.anchoranalysis.test.TestLoader: Creates a new test-data loader finding "src/test/resources" using the Maven working directory
createFromMavenWorkingDirectory(String) - Static method in class org.anchoranalysis.test.TestLoader: Creates a new test-data loader finding "src/test/resources/PLUS_SOMETHING" using the Maven working directory
createFromNotObjects(ObjectCollection, Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFromObjects: We look for space NOT in the objects, and create channel to display it
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.RejectIfNotConnected
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Duplicate
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.SortByFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.NotInContainer
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZ
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZWithinContainer
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.FlattenZ
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.DrawLineAlongConvexHull
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Filter
createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
createFromObjects(ObjectCollection, Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFromObjects: We look for space IN objects, and create channel to display it
createFromOutputter(String, OutputterChecked) - Static method in class org.anchoranalysis.io.generator.tabular.CSVWriter: Creates and starts a CSVWriter if it's allowed, otherwise returns Optional.empty().
createFromOverlays(ColoredOverlayCollection, IdentifierGetter<Overlay>, IdentifierGetter<ObjectWithProperties>) - Static method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributesFactory
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromChannel
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
createFromStack(Stack) - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
createFromStack(Stack) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
createFromStack(Stack) - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ColorConverterBase
createFromString(String) - Static method in class org.anchoranalysis.spatial.axis.AxisTypeConverter: Maps a string of x, y, z (case ignored) to a corresponding axis type
createFromTupleDuplicate(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.Extent: Createss an extent from a point (duplicating the point for internal use)
createFromTupleReuse(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.Extent: Creates from a point that is reused internally (without duplication)
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.And
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase: Creates masks from some combination of two masks
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.IfHighLow
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Or
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Xor
createGrayscaleByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageFactory
createGroupMap(ConsistentChannelChecker) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Creates a map for the storing an aggregate-data-object for each group.
createGroupMap(ConsistentChannelChecker) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
createGroupMap(ConsistentChannelChecker) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
createHashMapToId() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
createHeaders() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
createHeaders() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
createHeaders(boolean) - Method in class org.anchoranalysis.plugin.image.task.feature.GenerateLabelHeadersForCSV: Creates the label-headers (the headers for columns not associated with features)
createHistogramIgnoreZero(Channel, ObjectMask, boolean) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
createIdArr() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
createIdHashMap() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
createImageDim() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
createInitialized(Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
createInitParams(Optional<SharedObjects>, Optional<EnergyStack>) - Static method in class org.anchoranalysis.image.feature.session.InitParamsHelper
createInitParams(InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
createInitParams(InputOutputContext, Optional<NamedProvider<Stack>>, Optional<NamedProvider<ObjectCollection>>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
createInitParams(InputForMPPBean, InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
createInputContext() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments: Creates an input-context, reusing parameters from the experiment-execution
createInputProcessContext(Optional<String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
createInputProcessContext(Optional<String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
createInt() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
createInt(Voxels<UnsignedIntBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for UnsignedIntBuffer
createInt(Voxels<UnsignedIntBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create voxels-assigner for UnsignedIntBuffer.
createInt(BoundingBox) - Static method in class org.anchoranalysis.image.voxel.BoundedVoxelsFactory
createInt(Extent, IntFunction<UnsignedIntBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create voxels-arithmethic for UnsignedIntBuffer
createIntersectionComplement(ColoredOverlayCollection, ColoredOverlayCollection) - Static method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
createInverted() - Method in class org.anchoranalysis.image.core.mask.Mask
createInverted() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues: Inverts the values so OFF becomes ON, and vice-versa
createKernelFactoryNames() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
createKeyValueParams() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: returns the associated KeyValueParams or an empty set, if no params are associated with the energyScheme
createLabelledChannel(BoundedList<T>, Optional<Map<Integer, T>>) - Method in class org.anchoranalysis.image.core.object.label.LabelObjects: Creates a channel that contains a unique integer (label) for each element's object-representation.
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorScheme: Creates a list of colors of particular size.
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.HSB
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.VeryBright
createListChildFeatures() - Method in class org.anchoranalysis.feature.bean.Feature: Returns a list of Features that exist as bean-properties of this feature, either directly or in lists.
createListMembershipWithFlags() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
createManifestDescription() - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
createManifestDescription() - Method in class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
createManifestDescription() - Method in class org.anchoranalysis.io.generator.serialized.SerializedGenerator
createManifestDescription() - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
createManifestDescription() - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
createManifestDescription() - Method in class org.anchoranalysis.io.generator.tabular.CSVGenerator
createManifestDescription() - Method in class org.anchoranalysis.io.generator.text.StringGenerator
createManifestDescription() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
createManifestDescription() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
createManifestDescription(String) - Static method in class org.anchoranalysis.io.generator.collection.CollectionGenerator
createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.Autoname
createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromMetadata
createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
createMapToIndex() - Method in class org.anchoranalysis.feature.name.FeatureNameList: Creates a map from the feature-names to their indices in the list
createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>, CreateException>, Dimensions, boolean, double) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.EllipsoidFactory
createMarkEllipsoidLeastSquares(ObjectMask, Dimensions, boolean, double) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.EllipsoidFactory: Creates a MarkEllipsoid using least-squares fitting to the points on the outline of an object-mask
createMarkFromPoint(Point3d, int, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.MarkConicFactory
createMarkFromPoint(Point3i, int, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.MarkConicFactory
CreateMarkFromPoints - Class in org.anchoranalysis.mpp.bean.points
CreateMarkFromPoints() - Constructor for class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
createMarkFromPoints3f(List<Point3f>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
createMarkFromPoints3i(List<Point3i>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
createMaskOff(Dimensions) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to OFF
createMaskOff(Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to OFF
createMaskOn(Dimensions) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to ON
createMaskOn(Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory: Creates a binary-mask for specific dimensions with all voxels set to ON
createMerged(ColoredMarks) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
createMerged(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
createMerged(OverlayCollection) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
createMessageForDscr(String) - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
createMessageForDscr(String) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
createMessageForDscr(String) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Creates a message for the exception from the description
createMessageForDscr(String) - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
createMinusOne() - Method in class org.anchoranalysis.spatial.Extent: Creates a new Extent with each dimension decreased by one
createMockFeatureWithCalculation() - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture: Creates a mock-feature (using a mock-FeatureCalculation under the hood) which counts the number of pixels in an object
createMockFeatureWithCalculation(ToDoubleFunction<T>) - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture: Creates a mock-feature (using a mock-FeatureCalculation under the hood) with a result calculated using a lambda
createModelPool(ConcurrencyPlan) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled: Creates the model pool (to be used by multiple threads)
createModelPool(ConcurrencyPlan) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
createModelPool(ConcurrencyPlan) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
createNamedFeatureList(List<NamedBean<FeatureListProvider<T>>>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStoreFactory: Create a list of na
createNamedFeatureProviders(String, TestLoader) - Static method in class org.anchoranalysis.test.feature.plugins.FeaturesFromXmlFixture
createNames() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
createNecessaryDirectories(Path) - Static method in class org.anchoranalysis.annotation.io.WriterUtilities
CreateNew - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Creates a new channel with all values initialized to a constant (by default zero)
CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Creates a new empty collection of marks
CreateNew() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
CreateNew() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.CreateNew
CreateNew() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.CreateNew
createNewMarkPos(Orientation2D, Ellipse, RandomNumberGenerator, Dimensions, double, double, boolean) - Static method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
createNext(int, int) - Method in interface org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement.TableCreator
createNullErrorReporter() - Static method in class org.anchoranalysis.core.log.LogUtilities
createObject(Mask) - Static method in class org.anchoranalysis.image.core.object.factory.SingleObjectFromChannelFactory
createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.Overlay
createObjects() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.Comparer
createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
createOneToMany(Generator<T>, CheckedFunction<S, Stream<T>, ?>) - Static method in class org.anchoranalysis.io.generator.GeneratorBridge: Creates a bridge that maps ONE-TO-MANY from source to destination (i.e.
createOneToOne(Generator<T>, CheckedFunction<S, T, ?>) - Static method in class org.anchoranalysis.io.generator.GeneratorBridge: Creates a bridge that maps ONE-TO-ONE from source to destination (i.e.
createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
createOrReuse(Throwable) - Static method in exception org.anchoranalysis.core.exception.InitException
createOrReuse(T) - Method in class org.anchoranalysis.feature.session.strategy.replace.AlwaysNew
createOrReuse(T) - Method in class org.anchoranalysis.feature.session.strategy.replace.CacheAndReuseStrategy
createOrReuse(T) - Method in interface org.anchoranalysis.feature.session.strategy.replace.ReplaceStrategy
createOrReuse(T) - Method in class org.anchoranalysis.feature.session.strategy.replace.ReuseSingletonStrategy
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendFilePath
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendMarks
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendObjects
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
createPair(CreateCalculatorHelper, ImageInitParams, CacheTransferSourceCollection) - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
createPairsUnique() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
createPairsUnique() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
createParam(String, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
createParams(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelFaces
createParams(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxels
createParams(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
createParamsForImage(EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.KeyValueParamsForImageCreator
createPathDeriver(String, String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase: Creates a (rooted) file-path generator for a rootName and a regEx which matches three groups The first group should correspond to top-level folder for the project The second group should correspond to the unique name of the dataset.
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Determines the payload for any given or potential vertex
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
createPolicy() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
createPrecalc(DrawOverlay, ObjectWithProperties, Dimensions) - Static method in class org.anchoranalysis.overlay.writer.DrawOverlay
createPrefixerContext() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Determines the priority (and selection criteria) used to allow merges between neighbors
createPriority(ObjectVertex, ObjectVertex, Logger) - Method in interface org.anchoranalysis.plugin.image.object.merge.priority.Prioritizer
CreateProposalVisualization - Interface in org.anchoranalysis.mpp.proposer.visualization
CreateProposeVisualizationList - Class in org.anchoranalysis.mpp.proposer.visualization
CreateProposeVisualizationList() - Constructor for class org.anchoranalysis.mpp.proposer.visualization.CreateProposeVisualizationList
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
createRasters(AnnotationWithMarks, DisplayStack, Path, ColorScheme, Path, Logger, boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
createReducedFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
createRGB(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageFactory
createRGBMaskGenerator(DrawObject, DisplayStack, ColorList) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
createRGBStack(Channel, Channel, Channel, VoxelDataType) - Static method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
createRoot() - Static method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.Orientation
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
createRow(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
createSameSize(ChannelProvider, String, Channel) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Creates a new channel from a provider, making sure it's the same size as an an existing channel
createSameSize(MaskProvider, String, Channel) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker: Creates a new channel from a provider, making sure it's the same size as an an existing channel
createScaledMask(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.object.scaled.FromMask
createScaledMask(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in interface org.anchoranalysis.overlay.object.scaled.ScaledMaskCreator: Creates a scaled-version of the mask
createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.Overlay
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.AddToDefaults
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.NoneExcept
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Creates a new second-level SingleLevelOutputEnabled from the relevant set of strings.
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
createSequence(VoxelDataType) - Method in class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
createSession() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
createSet() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
createSet() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
createSet() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
createSetter(AnchorBean<?>) - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty
createSetter(AnchorBean<?>) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
createSetter(AnchorBean<?>) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, ResultsWriterOutputNames, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider<S>>>, ResultsWriterOutputNames, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider>>, ResultsWriterOutputNames, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask: Creates a shared-state for the duration of a particular input-job
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: Sets a new output-sequence for the series
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
createShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for UnsignedShortBuffer.
createShort(Voxels<UnsignedShortBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create voxels-assigner for UnsignedShortBuffer.
createShort(Extent, IntFunction<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create voxels-arithmethic for UnsignedShortBuffer
createSingle(CreateCalculatorHelper, ImageInitParams, BoundReplaceStrategy<FeatureInputSingleObject, CacheAndReuseStrategy<FeatureInputSingleObject>>) - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
createSingle(T, Function<T, BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundedList: Creates for a single element, using its current bounding-box.
createStack(List<RGBStack>, ChannelFactorySingleType) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.RasterArranger
CreateStackFromBufferedImage - Class in org.anchoranalysis.image.core.stack.bufferedimage
createStackSequenceForSeries(int) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
createStatistics() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
createStatistics() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
createStatistics() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
createStatistics() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.mpp.bean.mark.MarkRegion
createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.MaxNonZero
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
createStatisticsHeaderNames() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
createStatisticsHeaderNames() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
createStatisticsHeaderNames() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs: The headers needed to create statistics
createSubdirectory(String, ManifestDirectoryDescription, boolean) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: Maybe creates a subdirectory for writing to.
createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in interface org.anchoranalysis.io.output.writer.Writer: Maybe creates a subdirectory for writing to.
createSubset(IntPredicate) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
createSubset(List<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: A subset of the collection identified by particular indices.
createSubsetFromIDs(IntPredicate) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
createUninitialised(Dimensions, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
createUninitialized(Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
createUniqueNamesSorted() - Method in class org.anchoranalysis.feature.name.FeatureNameList
createValues() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
createValues() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.DirectionVectorBean: Creates a vector in a particular direction
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
createVector3d() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
createWithConsoleFallback(OutputterChecked, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination: Creates a logger for this destination - and if anything goes wrong reporting fallback into the console.
createWithDir(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CompressTIFF
createWithDir(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CopyFilesMethod
createWithDir(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.SimpleCopy
createWithLogFallback(OutputterChecked, MessageLogger, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination: Creates a logger for this destination - and if anything goes wrong reporting fallback into a log.
createWithoutColor(ObjectCollection, IdentifierGetter<ObjectMask>) - Static method in class org.anchoranalysis.overlay.collection.OverlayCollectionObjectFactory
createWithoutColor(MarkCollection, RegionMembershipWithFlags) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
createWithPrefix(DirectoryWithPrefix, MultiLevelOutputEnabled, OutputWriteSettings, Optional<WriteOperationRecorder>, Optional<MultiLevelRecordedOutputs>, boolean) - Static method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates a bound output-manager from an existing OutputManager with a prefix.
createWithRangeLimits(Iterator<T>, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter: Creates or gets an instance of IFormatWriter which dictates the file format to use for writing.
createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMETiff
createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMEXML
createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
cross(Vector3d, Vector3d) - Static method in class org.anchoranalysis.spatial.point.Vector3d
CSVGenerator<T> - Class in org.anchoranalysis.io.generator.tabular
CSVGenerator(String) - Constructor for class org.anchoranalysis.io.generator.tabular.CSVGenerator
CSVReporterAggregated - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter: Outputs statistics on current energy / kernel acceptance etc.
CSVReporterAggregated() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
CSVReporterBest - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter: Outputs a CSV with statistics on the configuration/energy only the best configuration state changes.
CSVReporterBest() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
CSVReporterUtilities - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
CSVRow - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv: A row of the CSV File
CSVRow(ColumnDefinition) - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
csvString() - Method in class org.anchoranalysis.math.histogram.Histogram
CSVWriter - Class in org.anchoranalysis.io.generator.tabular
CUBIC_MICRO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
CUBIC_NANO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
currentStateDescription() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
currentTemperature() - Method in class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
currentTemperature() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
currentTemperature() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.NoAnnealing
customizeExperimentTemplate(ExperimentExecutor, CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
CustomManagerFromPath - Class in org.anchoranalysis.launcher.executor.selectparam.path: Loads a custom-manager from a path
CustomManagerFromPath(Path) - Constructor for class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
CutBelowThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the threshold into the bin just below the threshold value
CutBelowThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
CVFindContours - Class in org.anchoranalysis.plugin.opencv: Wrapper around Open CV's findContours function
CVInit - Class in org.anchoranalysis.plugin.opencv: Provides for initialization of the JavaCPP bridge to OpenCV.

D

dataType() - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
dataType() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Data-type of each voxel in the buffer.
dataType() - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
dataType() - Method in class org.anchoranalysis.image.voxel.Voxels
DataTypeMaxIntensity<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity: The maximum-intensity allowed by the data-type of the stack (e.g.
DataTypeMaxIntensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.DataTypeMaxIntensity
DebugDependentProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor: Executes different processors depending on whether we are in debug mode or not
DebugDependentProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
decode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection: Decodes a chain-code into a point
decodeConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
DecodeLabels<T> - Class in org.anchoranalysis.image.core.object.label: Decodes a labelled raster into derived objects or object-like elements.
DecodeLabels(Voxels<?>, int, int, DecodeLabels.CreateElementFromScaledObject<T>) - Constructor for class org.anchoranalysis.image.core.object.label.DecodeLabels
DecodeLabels.CreateElementFromScaledObject<T> - Interface in org.anchoranalysis.image.core.object.label: Creates an element from the scaled-object and its index
DecomposeIntoConnectedComponents - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected: Ensures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.
DecomposeIntoConnectedComponents() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
decrement() - Method in class org.anchoranalysis.math.arithmetic.Counter
decrementX() - Method in class org.anchoranalysis.spatial.point.Tuple3i
decrementX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
decrementY() - Method in class org.anchoranalysis.spatial.point.Tuple3i
decrementY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
decrementZ() - Method in class org.anchoranalysis.spatial.point.Tuple3i
decrementZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
deepCopy() - Method in class org.anchoranalysis.core.color.ColorList
deepCopy() - Method in class org.anchoranalysis.feature.energy.EnergyTotal
deepCopy() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
deepCopy() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Make a deep copy (except the energyScheme which is reused).
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy: Creates a deep-copy of the marks
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
deepCopy() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
deepCopy() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
deepCopy() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
deepCopy() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
Default - Class in org.anchoranalysis.io.bioformats.bean.options
Default() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.Default
DEFAULT_COLOR_SET_GENERATOR - Static variable in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
DEFAULT_FUNC_NUM_PIXELS - Static variable in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture
DEFAULT_IMAGE_INPUT_NAME - Static variable in class org.anchoranalysis.mpp.io.input.MultiInput
defaultColorIndexFor(int) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
defaultExperimentOrCustom(CommandLine, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.experiment.ExperimentFactory: Chooses either a path to the default-experiment or a path to a custom experiment.
DefaultFindChildStrategy - Class in org.anchoranalysis.feature.session.strategy.child: The default strategy for finding children by always directly taking (or creating a child-cache) as necessary.
DefaultInstance - Annotation Type in org.anchoranalysis.bean.annotation: Indicates a default bean-instance is available.
defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: If specified, default rules for determine which outputs are enabled or not.
defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.task.Task: If specified, default rules for determine which outputs are enabled or not.
defaultOutputs() - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks: If specified, default rules for determine which outputs are enabled or not.
defaultOutputs() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
defaultOutputs() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
defaultOutputs() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Define - Class in org.anchoranalysis.bean.define: A bean where the definitions of many different NamedBeans can be specified.
Define<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
Define() - Constructor for class org.anchoranalysis.bean.define.Define
Define() - Constructor for class org.anchoranalysis.feature.bean.list.Define
Define(List<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.Define
Define(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.list.Define
DefineAdder - Interface in org.anchoranalysis.bean.define.adder: Adds bean-definitions to a Define class
DefineAdderBean - Class in org.anchoranalysis.bean.define.adder
DefineAdderBean() - Constructor for class org.anchoranalysis.bean.define.adder.DefineAdderBean
DefineAdderUtilities - Class in org.anchoranalysis.bean.define.adder
DefineAdderWithPrefixBean - Class in org.anchoranalysis.bean.define.adder: Adds a prefix
DefineAdderWithPrefixBean() - Constructor for class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
DefinedNamed<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
DefinedNamed() - Constructor for class org.anchoranalysis.feature.bean.list.DefinedNamed
DefineFactory - Class in org.anchoranalysis.bean.define: Creates a new Define
DefineFactory() - Constructor for class org.anchoranalysis.bean.define.DefineFactory
DefineOutputter - Class in org.anchoranalysis.mpp.segment.bean.define: After using applying a Define on inputs, output produced entities (images, histograms, objects etc.)
DefineOutputter() - Constructor for class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
DefineOutputterImage - Class in org.anchoranalysis.mpp.segment.bean.define: Helper for tasks that uses a Define in association with an input to execute some tasks, and then outputs results *
DefineOutputterImage() - Constructor for class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterImage
DefineOutputterMPP - Class in org.anchoranalysis.mpp.segment.bean.define
DefineOutputterMPP() - Constructor for class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
DefineOutputterMPP.OperationWithInitParams<T> - Interface in org.anchoranalysis.mpp.segment.bean.define
DefineOutputterMPPWithEnergy - Class in org.anchoranalysis.plugin.mpp.bean.define: Like a Define but outputs also MPP-related data objects and an energy-stack.
DefineOutputterMPPWithEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy
DefineOutputterMPPWithEnergy.OperationWithEnergyStack<T,S> - Interface in org.anchoranalysis.plugin.mpp.bean.define
DefineOutputterWithEnergy - Class in org.anchoranalysis.plugin.mpp.bean.define
DefineOutputterWithEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
DefineSingle<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
DefineSingle() - Constructor for class org.anchoranalysis.feature.bean.list.DefineSingle
delegate() - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
delete(Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationDeleter: Deletes all files at this path (or any other paths derived from this one
delete(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationDeleter
delete(Path) - Method in class org.anchoranalysis.annotation.io.SimpleAnnotationDeleter
delete(BoundingBox, T) - Method in class org.anchoranalysis.spatial.rtree.RTree
DensityKernel - Class in org.anchoranalysis.image.voxel.kernel.density
DensityKernel(int, BinaryValuesByte, double) - Constructor for class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
deriveArray() - Method in class org.anchoranalysis.spatial.Extent: Derives an three-element array with each dimension in the extent.
deriveAssociatedFiles() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
deriveBoundingBox() - Method in class org.anchoranalysis.spatial.box.PointRange
deriveBoundingBoxNoCheck() - Method in class org.anchoranalysis.spatial.box.PointRange: Like PointRange.deriveBoundingBox() but doesn't throw an exception if no points exist.
deriveConnectedByte(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.unionfind.ConnectedComponentUnionFind: Converts binary-voxels (byte) into connected components.
deriveConnectedInt(BinaryVoxels<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.unionfind.ConnectedComponentUnionFind: Converts binary-voxels (int) into connected components.
DerivedObject - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
DerivedObject() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
DeriveElementsFromSequencedDirectory<T> - Class in org.anchoranalysis.io.manifest.directory.sequenced: Derives elements of type T from a directory containing a sequence of files.
DeriveElementsFromSequencedDirectory(SequencedDirectory) - Constructor for class org.anchoranalysis.io.manifest.directory.sequenced.DeriveElementsFromSequencedDirectory
deriveExtent() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
deriveFromDelegate(FeatureInputSingleObject, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
deriveFromDelegate(T, U) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
DeriveFromPair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Embeds each feature in a FeatureDeriveFromPair feature (first, second or merge) and prepends with a string.
DeriveFromPair() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
deriveInputsStartBatch(ObjectCollection, EnergyStack, boolean, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Derives a list of inputs (i.e.
deriveLabels(T, int) - Method in interface org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects.LabelsForInput: Calculates labels for a given input (and index)
deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.NormalizedPath
deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
deriveName(Collection<File>, String, Logger) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.patternspan.PatternSpan
deriveName(Collection<File>, String, Logger) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
deriveObject() - Method in interface org.anchoranalysis.image.core.object.seed.Seed
deriveObject() - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.mark.Mark: Create an object-mask representation of the mark (i.e.
deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
deriveObject(BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
deriveObject(BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
deriveObject(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Creates an object-mask for all the voxels inside the bounding-box satisfying the predicate.
deriveObjects() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
deriveObjects(Dimensions, RegionMembershipWithFlags) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
derivePath(DerivePath, Path) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.PathFromGenerator
derivePointsLocal() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates a list of all ON voxels as points, using local coordinates i.e.
deriveRootedPath(Path, String, boolean, boolean) - Static method in class org.anchoranalysis.plugin.io.input.path.RootedFilePathUtilities
deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase: Derive scores given the value, mean and standard-deviation
deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.ZScore
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
deriveStack(boolean) - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Derives a Stack from the display-stack that will be converted to 8-bit if necessary.
deriveStackDuplicate() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MeanAcrossObjects
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
deriveSubdirectory(String, ManifestDirectoryDescription, boolean) - Method in class org.anchoranalysis.io.output.outputter.Outputter: Creates a new Outputter by appending a relative folder-path to the current Outputter
deriveSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Derives a bound-output-manager for a (possibly newly created) subdirectory of the existing manager
deriveUnsignedBytePredicate() - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes: Derives a predicate with a different interface for operating on UnsignedByteBuffer.
deriveUnsignedByteProcessor() - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes: Derives a processor with a different interface for operating on UnsignedByteBuffer.
describe() - Method in class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
describe() - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam: A string that can be displayed to the user to describe this particular SelectParam.
describe() - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
describe() - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
describe() - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph: Generates a string describing the entire graph (vertices and edges)
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer: Returns a string summarizing this item
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
describe(boolean) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Describes the graph in a multi-line string.
describe(String) - Method in class org.anchoranalysis.plugin.io.summarizer.FrequencyMap
describeAcceptedClasses() - Method in interface org.anchoranalysis.bean.initializable.property.PropertyDefiner
describeAcceptedClasses() - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
describeBean() - Method in class org.anchoranalysis.bean.AnchorBean: A (maybe longer) description identifying the bean and perhaps its key parameters.
describeBean() - Method in class org.anchoranalysis.feature.bean.Feature
describeBean() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
describeBean() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
describeBean() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
describeBean() - Method in class org.anchoranalysis.mpp.feature.mark.MarkPairCollection
describeBean() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
describeBean() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
describeBean() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
describeBean() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
describeChildren() - Method in class org.anchoranalysis.bean.AnchorBean: Generates a string describing the children of the current bean.
describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph: Generates a string to describe a potential merge
describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
DescribeGraph - Class in org.anchoranalysis.plugin.image.object.merge: Logs descriptions of the graph
DescribeGraph(NeighborGraph, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.DescribeGraph: Constructor
describeLast() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
describeMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph
describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
describeParams() - Method in class org.anchoranalysis.feature.bean.Feature
describeParams() - Method in class org.anchoranalysis.feature.bean.operator.Constant
describeParams() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
describeParams() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
describePropertiesFriendly() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: A string that uniquely identifies all properties in the bean, but friendly to humans
describeTo(boolean) - Method in class org.anchoranalysis.core.graph.TypedEdge: Describes the edge by showing the to vertex, and optionally the payload.
description() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory: A description of this directory for the manifest.
description(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch: Match a file whose manifest-description has a specific function.
description(String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DirectoryMatch
description(String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch: Match a file whose manifest-description has a specific function and type.
description(String, String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch: Match a file whose manifest-description has either of two specific function and a specific type.
descriptionAndOutputName(String, String, String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch: Match a file whose manifest-description has either of two specific function and a specific type and whose output-name matches a specific value.
descriptionForList(String) - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem: A string description of all the items of the list concatenated together with a character in between
descriptionLong() - Method in class org.anchoranalysis.feature.bean.Feature
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Constant
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Reference
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Sum
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.NormalizedRange
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
DescriptionMatch - Class in org.anchoranalysis.io.manifest.finder.match
descriptionWithCustomName() - Method in class org.anchoranalysis.feature.bean.Feature
DescriptiveNameContainsImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
DescriptiveNameContainsImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
DeserializationFailedException - Exception in org.anchoranalysis.core.serialize
DeserializationFailedException(Exception) - Constructor for exception org.anchoranalysis.core.serialize.DeserializationFailedException
DeserializationFailedException(String) - Constructor for exception org.anchoranalysis.core.serialize.DeserializationFailedException
DeserializationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.serialize.DeserializationFailedException
deserialize(Path) - Method in interface org.anchoranalysis.core.serialize.Deserializer
deserialize(Path) - Method in class org.anchoranalysis.core.serialize.KeyValueParamsDeserializer
deserialize(Path) - Method in class org.anchoranalysis.core.serialize.ObjectInputStreamDeserializer
deserialize(Path) - Method in class org.anchoranalysis.core.serialize.XStreamDeserializer
deserialize(Path) - Method in class org.anchoranalysis.mpp.io.marks.MarkCollectionDeserializer
DeserializedManifest - Class in org.anchoranalysis.plugin.io.manifest: A manifest after being deserialized from the file-system.
DeserializedManifest(File, ManifestDeserializer) - Constructor for class org.anchoranalysis.plugin.io.manifest.DeserializedManifest
deserializeManifest(File) - Method in interface org.anchoranalysis.io.manifest.deserializer.ManifestDeserializer
deserializeManifest(File) - Method in class org.anchoranalysis.io.manifest.deserializer.SimpleManifestDeserializer
Deserializer<T> - Interface in org.anchoranalysis.core.serialize
DestinationChannelForIndex - Interface in org.anchoranalysis.io.bioformats: Selects a destination-channel for the byte-copier, given an index
destinationPath(Path, Path, File, int) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming: Returns the output path (destination to to be copied to) for a given single file
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.RemoveWhitespace
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch
destinationPathRelative(Path, Path, File, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
destinationPathRelative(Path, Path, File, int) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming: Calculates the relative-output path (to be appended to destDir)
destinationPathRelative(Path, Path, File, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
destinationPathRelative(Path, Path, File, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions: Returns a list of channel-names or null if they are unavailable
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
determineCost() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate: Merges
determineInputType(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Finds a common input-type for two classes, throwing an exception if the two types aren't compatible.
determineInputType(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Finds a common input-type for classes in the list, throwing an exception if any two types aren't compatible.
Develop - Class in org.anchoranalysis.plugin.mpp.experiment.bean.define: Derives various types of outputs (images, histograms etc.) from MultiInputs.
Develop() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
Difference - Class in org.anchoranalysis.plugin.image.feature.bean.score
Difference() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.Difference
DifferenceCalculateLevelStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.score: Similar to Difference but calculates the width as the standard-deviation of the histogram
DifferenceCalculateLevelStandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
differenceFrom(Path, Path) - Static method in class org.anchoranalysis.core.system.path.PathDifference: Finds the difference between a path and a base
dilate(boolean, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Grow bounding-box by 1 pixel in all directions
dilate(BinaryVoxels<UnsignedByteBuffer>, boolean, int, Optional<Voxels<UnsignedByteBuffer>>, int, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation
dilate(BinaryVoxels<UnsignedByteBuffer>, int, Optional<Voxels<UnsignedByteBuffer>>, int, Optional<AcceptIterationConditon>, DilationKernelFactory) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation: Performs a morpholgical dilation operation
Dilate - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Performs an dilation morphological operation on a binary-image
Dilate - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological: Dilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
Dilate() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
Dilate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
DilationKernel3 - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
DilationKernel3(BinaryValuesByte, boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3
DilationKernel3ZOnly - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
DilationKernel3ZOnly(BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3ZOnly
DilationKernelFactory - Class in org.anchoranalysis.image.voxel.object.morphological
DilationKernelFactory(SelectDimensions, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.object.morphological.DilationKernelFactory
dimensionIndexFor(AxisType) - Static method in class org.anchoranalysis.spatial.axis.AxisTypeConverter: An index representing each dimension (0 for X, 1 for Y, 2 for Z)
dimensions() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The image-dimensions associated with the energy-stack.
dimensions() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
dimensions() - Method in class org.anchoranalysis.image.core.channel.Channel
dimensions() - Method in class org.anchoranalysis.image.core.mask.Mask
dimensions() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
dimensions() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
dimensions() - Method in class org.anchoranalysis.image.core.stack.Stack
dimensions() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
dimensions() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
dimensions() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
dimensions() - Method in interface org.anchoranalysis.mpp.probmap.PointSampler
dimensions() - Method in class org.anchoranalysis.mpp.probmap.ProbMapObjects
dimensions() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
dimensions() - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
Dimensions - Class in org.anchoranalysis.image.core.dimensions: The dimensions of an image (in voxels), together with the image resolution.
Dimensions(int, int, int) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions: Construct with an explicit extent and default resolution (1.0 for each dimension)
Dimensions(Extent) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions: Construct with an explicit extent and default resolution (1.0 for each dimension)
Dimensions(Extent, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions
Dimensions(ReadableTuple3i) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions: Construct with an explicit extent and default resolution (1.0 for each dimension)
DimensionsChecker - Class in org.anchoranalysis.plugin.image.channel
DimensionsCreator - Class in org.anchoranalysis.io.bioformats
DimensionsCreator(IMetadata) - Constructor for class org.anchoranalysis.io.bioformats.DimensionsCreator
dimensionsForSeries(int) - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
dimensionsForSeries(int) - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
dimensionsOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
DimensionsProvider - Class in org.anchoranalysis.image.bean.provider
DimensionsProvider() - Constructor for class org.anchoranalysis.image.bean.provider.DimensionsProvider
dimensionsRequired() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
DirectAssignMode<S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode: Directly assigns a state for every optimisation step
DirectAssignMode() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
DirectAssignMode(ExtractScoreSize<S>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
DirectionVector - Class in org.anchoranalysis.image.core.orientation
DirectionVector() - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector
DirectionVector(double, double, double) - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector
DirectionVector(AxisType) - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector: Creates a direction aligned to a particular axis.
DirectionVector(Tuple3d) - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector
DirectionVectorBean - Class in org.anchoranalysis.image.bean.spatial.direction: A bean that creates a DirectionVector
DirectionVectorBean() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.DirectionVectorBean
DirectoryDepth - Class in org.anchoranalysis.plugin.io.bean.input.files.provider: Lists all directories to a certain depth
DirectoryDepth() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
DirectoryMatch - Class in org.anchoranalysis.io.manifest.finder.match
DirectoryStructure - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer: Reuses the directories between a path and its root to form the output - and also the filename.
DirectoryStructure() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
DirectoryWithPrefix - Class in org.anchoranalysis.io.output.path.prefixer
DirectoryWithPrefix(Path) - Constructor for class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
DirectoryWithPrefix(Path, String) - Constructor for class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
dirtyInitialization() - Static method in class org.anchoranalysis.launcher.DirtyInitializer: Dirty initialisation work done that must be done every time we initialise an application that will use the Anchor platform
DirtyInitializer - Class in org.anchoranalysis.launcher: Inelegant initialisation methods that should be done in the plugins themselves, when a proper framework exists for Initialising plugins
disableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta: Assigns additional outputs to disable.
DiscardOutliers - Class in org.anchoranalysis.plugin.image.bean.object.filter.dependent: Calculates features values for all objects, and discards any object less than quantile - (minRatio * stdDev)
DiscardOutliers() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
DisplayStack - Class in org.anchoranalysis.image.core.stack: Stack that contains 1 or 3 channels so that we and display it as either or RGB unsigned 8-bit image
distance(Mark, Mark) - Method in class org.anchoranalysis.mpp.bean.mark.MarkDistance
distance(Mark, Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceAbstractPosition
distance(Mark, Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceRadii
distance(BoundingBox, BoundingBox, boolean) - Static method in class org.anchoranalysis.spatial.box.BoundingBoxDistance
distance(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d
distance(Point3d) - Method in class org.anchoranalysis.spatial.point.Point3d: Euclidean distance from this point to another
distance(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
distance(Point3f) - Method in class org.anchoranalysis.spatial.point.Tuple3f
distance(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i
distance(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
DistanceCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
DistanceCondition(Optional<UnitValueDistance>, boolean, MessageLogger) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.DistanceCondition
DistanceIndex - Class in org.anchoranalysis.image.core.outline.traverser.path: A distance, and the index the point came from
DistanceIndex(int, int) - Constructor for class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
distanceMax(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i: The maximum distance across any axis
distanceMaxToHeadTail(Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels: The maximum-distance of a point to the closest contiguous-path
DistancePhysical - Class in org.anchoranalysis.image.bean.unitvalue.distance
DistancePhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
distanceSquared(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d
distanceSquared(Point3d) - Method in class org.anchoranalysis.spatial.point.Point3d
distanceSquared(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution: The square of the distance between two points taking account image-resolution.
distanceSquared(Point3f) - Method in class org.anchoranalysis.spatial.point.Tuple3f
distanceSquared(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3d: Square of Euclidean distance from this point to another
distanceSquared(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i
distanceSquared(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Resolution: The square of the distance between two points taking account image-resolution.
distanceSquaredTo(Point3i) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
distanceSquaredZRelative(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
distanceSquaredZRelative(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
DistanceToContiguousPath - Class in org.anchoranalysis.image.core.outline.traverser.path
DistanceTransform3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance: Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
DistanceTransform3D() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
DistanceTransformForEachObject3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance: Like DistanceTransform3D but applies the distance transform separately for each object in a collection.
DistanceTransformForEachObject3D() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
DistanceVoxels - Class in org.anchoranalysis.image.bean.unitvalue.distance
DistanceVoxels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
DistanceVoxels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
distanceZRelative(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
div(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
div(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
div(AggIDCounter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
divide(int) - Method in class org.anchoranalysis.spatial.Extent
Divide<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
Divide() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
divideBy(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
divideBy(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
divideBy(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
DivideByConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
DivideByConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
divideByZeroReplace(double, double, double) - Static method in class org.anchoranalysis.math.arithmetic.DoubleUtilities: Replaces a value with a constant if the divider is 0
Divider - Class in org.anchoranalysis.experiment.log: Creates a line of text that span a certain width with a repeated character, optionally containing a label.
Divider() - Constructor for class org.anchoranalysis.experiment.log.Divider: A banner using dashes.
Divider(char) - Constructor for class org.anchoranalysis.experiment.log.Divider: A banner using a particular repeated character.
DO_NOT_CHANGE_EXISTING - org.anchoranalysis.image.core.channel.convert.ConversionPolicy
doDuplicate(PointListBase) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
doesClassInheritFromAny(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.task.InputTypesExpected: Does the childclass inherit from any one of expected input-types
doesPathExist(String) - Method in class org.anchoranalysis.test.TestLoader: Does a resource exist with a particular folderPath + fileName
doesPathExist(String, String) - Method in class org.anchoranalysis.test.TestLoader: Does a resource exist with a particular folderPath + fileName
doFind(Manifest) - Method in interface org.anchoranalysis.io.manifest.finder.Finder
doFind(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
doFind(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
doFind(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
doInitFor(Object, Object, Object, Logger) - Method in interface org.anchoranalysis.bean.initializable.property.PropertyDefiner
doInitFor(Object, Object, Object, Logger) - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
doJobOnInput(InputBound<AnnotationWithStrategy<S>, AggregateSharedState>) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
doJobOnInput(InputBound<NamedChannelsInput, SharedStateSelectedSlice>) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
doJobOnInput(InputBound<NamedChannelsInput, S>) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
doJobOnInput(InputBound<ProvidesStackInput, GroupedSharedState<S, T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
doJobOnInput(InputBound<ProvidesStackInput, SharedStateFilteredImageOutput<T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
doJobOnInput(InputBound<FileInput, CSVWriter>) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
doJobOnInput(InputBound<MultiInput, CSVWriter>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
doJobOnInput(InputBound<MultiInput, ExperimentState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
doJobOnInput(InputBound<AnnotationComparisonInput<ProvidesStackInput>, SharedState<T>>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
doJobOnInput(InputBound<StackSequenceInput, SharedStateSegmentInstance<T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
doJobOnInput(InputBound<ManifestCouplingDefinition, NoSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
doJobOnInput(InputBound<FromCSVInput, FromCSVSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
doJobOnInput(InputBound<S, NoSharedState>) - Method in class org.anchoranalysis.experiment.bean.task.HelloWorld
doJobOnInput(InputBound<T, SharedStateExportFeatures<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
doJobOnInput(InputBound<T, Summarizer<S>>) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
doJobOnInput(InputBound<T, S>) - Method in class org.anchoranalysis.experiment.bean.task.Task: Performs the task on a particular input.
doJobOnInput(InputBound<T, S>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
doOperation(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.mpp.feature.bean.mark.PxlListOperationFromMark
doSeedsIntersect() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
doSeedsIntersectWithContainingMask(ObjectMask) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
doStack(InputBound<NamedChannelsInput, NoSharedState>, NoSharedState, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
doStack(InputBound<NamedChannelsInput, NoSharedState>, OutputSequenceIndexed<Stack, String>, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
doStack(InputBound<NamedChannelsInput, OutputSequenceIncrementing<Stack>>, NoSharedState, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
doStack(InputBound<NamedChannelsInput, S>, U, int, int, InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask: Processes one stack from a series.
dot(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
DotProductOrientationToVector - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
DotProductOrientationToVector() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.DotProductOrientationToVector
doubleFromFloat(Point2f) - Static method in class org.anchoranalysis.spatial.point.PointConverter
doubleFromFloat(Point3f) - Static method in class org.anchoranalysis.spatial.point.PointConverter
doubleFromInt(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
doubleFromInt(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
DoubleRange() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
DoubleUtilities - Class in org.anchoranalysis.math.arithmetic: Utilities for arithmetic operations involving type double
downcast() - Method in class org.anchoranalysis.feature.bean.Feature: Downcasts the feature
DrawLineAlongConvexHull - Class in org.anchoranalysis.plugin.imagej.bean.object.provider: Draws a lines between successive points on the convex-hull of an object.
DrawLineAlongConvexHull() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.provider.DrawLineAlongConvexHull
DrawObject - Class in org.anchoranalysis.overlay.bean: Draws an object-mask on a RGB-stack
DrawObject() - Constructor for class org.anchoranalysis.overlay.bean.DrawObject
DrawOverlay - Class in org.anchoranalysis.overlay.writer: Draws an overlay onto a RGB-stack, including precalculated overlays.
DrawOverlay() - Constructor for class org.anchoranalysis.overlay.writer.DrawOverlay
dropKey() - Method in exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Ignores the name in the exception
dropZ() - Method in class org.anchoranalysis.spatial.point.Point3d: Creates a new point with identical x and y, but with z set to 0
DualMarks - Interface in org.anchoranalysis.annotation.mark: Two mark-collections, one considered accepted and the other rejected.
DualMarksAnnotation<T> - Class in org.anchoranalysis.annotation.mark: An annotation that consists of two sets of marks, accepted and rejected.
DualMarksAnnotation() - Constructor for class org.anchoranalysis.annotation.mark.DualMarksAnnotation
DualStack - Class in org.anchoranalysis.mpp.segment.optimization: Stores an EnergyStack together with a background stack.
DualStack(EnergyStack) - Constructor for class org.anchoranalysis.mpp.segment.optimization.DualStack: Creates to infer a background from the energy-stack.
DualStack(EnergyStack, DisplayStack) - Constructor for class org.anchoranalysis.mpp.segment.optimization.DualStack
DualState<T> - Class in org.anchoranalysis.mpp.segment.optimization: Remembers the current state of type T and some best state (which was once set from the current state)
DualState() - Constructor for class org.anchoranalysis.mpp.segment.optimization.DualState
DualVoxelizedMarks - Class in org.anchoranalysis.plugin.mpp.segment.optimization: A transformation of one VoxelizedMarksWithEnergy into another
DualVoxelizedMarks(VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.DualVoxelizedMarks
DualWriterOperationRecorder - Class in org.anchoranalysis.io.manifest.operationrecorder: Allows two WriteOperationRecorder function together as if they are one
DualWriterOperationRecorder(WriteOperationRecorder, WriteOperationRecorder) - Constructor for class org.anchoranalysis.io.manifest.operationrecorder.DualWriterOperationRecorder
duplicate() - Method in class org.anchoranalysis.core.color.RGBColor
duplicate() - Method in class org.anchoranalysis.core.value.KeyValueParams
duplicate() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
duplicate() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
duplicate() - Method in class org.anchoranalysis.image.core.channel.Channel
duplicate() - Method in class org.anchoranalysis.image.core.mask.Mask
duplicate() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
duplicate() - Method in interface org.anchoranalysis.image.core.object.seed.Seed
duplicate() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
duplicate() - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
duplicate() - Method in class org.anchoranalysis.image.core.orientation.Orientation
duplicate() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
duplicate() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
duplicate() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
duplicate() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
duplicate() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
duplicate() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
duplicate() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
duplicate() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
duplicate() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures: Immutably creates entirely new duplicated features
duplicate() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
duplicate() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
duplicate() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Creates a deep copy of the current object, including deep-copying the associated buffer.
duplicate() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Deep copy, including duplicating object-masks
duplicate() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
duplicate() - Method in class org.anchoranalysis.image.voxel.Voxels
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: Deep copy the current object.
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
duplicate() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Deep-copy
duplicate() - Method in class org.anchoranalysis.math.histogram.Histogram
duplicate() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
duplicate() - Method in class org.anchoranalysis.math.moment.ImageMoments
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.Bound
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
duplicate() - Method in class org.anchoranalysis.mpp.mark.Mark
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.PointList
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
duplicate() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
duplicate() - Method in class org.anchoranalysis.plot.AxisLimits
duplicate() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
Duplicate - Class in org.anchoranalysis.plugin.image.bean.channel.provider
Duplicate - Class in org.anchoranalysis.plugin.image.bean.mask.provider
Duplicate - Class in org.anchoranalysis.plugin.image.bean.object.provider: Duplicates (deep copy) an object-collection.
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Duplicate
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Duplicate
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Duplicate
duplicateBean() - Method in class org.anchoranalysis.bean.AnchorBean: Creates a new bean that deep-copies every property value.
duplicateBean() - Method in class org.anchoranalysis.bean.define.Define
duplicateBean() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
duplicateBean() - Method in class org.anchoranalysis.bean.StringList: Duplicate the bean
duplicateBean() - Method in class org.anchoranalysis.bean.StringSet: Duplicate the bean
duplicateChangeExtent(Extent) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
duplicateChangeName(String) - Method in class org.anchoranalysis.feature.bean.Feature: Duplicates the feature as per AnchorBean.duplicateBean() but sets a particular custom-name
duplicateChangeResolution(Optional<Resolution>) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
duplicateChangeZ(int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
duplicateChangeZ(int) - Method in class org.anchoranalysis.spatial.Extent
duplicateChangeZ(int) - Method in class org.anchoranalysis.spatial.point.Point3i
duplicateChangeZ(int) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
duplicateDeep() - Method in class org.anchoranalysis.image.core.stack.Stack: Performs a deep copy of the stack, so that all channels are duplicated.
duplicateFlattenZ(int) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
duplicateForNewThread() - Method in interface org.anchoranalysis.image.feature.session.FeatureTableCalculator: Makes a copy of the feature-store for a new thread.
duplicateForNewThread() - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
duplicateForNewThread() - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
duplicateFresh() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
duplicateHelper(Feature<FeatureInput>) - Method in class org.anchoranalysis.feature.bean.Feature
duplicateHelper(KernelPosNeg<T>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
duplicateHelper(ConicFitterBase) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
duplicateShallow() - Method in class org.anchoranalysis.image.core.stack.Stack: Performs a shallow copy of the stack, so that all channels are reused.
duplicateShallow() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Shallow copy of objects

E

EachObjectIndependently - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine: Simply selects features directly from the list, and objects directly from the list passed.
EachObjectIndependently() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
EagerEvaluationStore<T> - Class in org.anchoranalysis.core.identifier.provider.store: Evaluates items via their Getter as soon as they are added
EagerEvaluationStore() - Constructor for class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
eccentricity(double, double) - Static method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity: Calculates eccentricity given two axes
EccentricityAxisAligned - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
EccentricityAxisAligned() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityAxisAligned
eccentricityForEllipsoid(double[], Orientation) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityAxisAligned
eccentricityForEllipsoid(double[], Orientation) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityGuessXYPlane
eccentricityForEllipsoid(double[], Orientation) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity: Calculates eccentricity in 3D-case
EccentricityGuessXYPlane - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
EccentricityGuessXYPlane() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityGuessXYPlane
EdgeAdderParameters - Class in org.anchoranalysis.image.voxel.neighborhood
EdgeAdderParameters(boolean) - Constructor for class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
EdgeFilterIJ - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
EdgeFilterIJ() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.EdgeFilterIJ
edgesMaybeDuplicates() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The edges in the graph, all of them, but with some edges possibly duplicated.
edgesUnique() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The edges in the graph, all of them, without any duplicates.
effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
EigenvalueAndVector - Class in org.anchoranalysis.math.moment: An eigen-value and its corresponding eigen-vector.
EigenvalueAndVector(double, DoubleMatrix1D) - Constructor for class org.anchoranalysis.math.moment.EigenvalueAndVector
eigenvalueNormalizedAsAxisLength() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector: A normalization of an eigen-value to represent axis-length.
eitherFunctionAndType(String, String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DescriptionMatch
elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
ElementSupplier<T> - Interface in org.anchoranalysis.io.output.writer: Creates or gets a element to output files together with a ElementWriter.
elementwiseOperation(ReadableTuple3i, ReadableTuple3i, IntBinaryOperator) - Static method in class org.anchoranalysis.spatial.point.Point3i: Applies an operation to each element across two points
ElementWriter<T> - Interface in org.anchoranalysis.io.output.writer: Writes an element (with or without an index) to the file system.
ElementWriterSupplier<T> - Interface in org.anchoranalysis.io.output.writer: Creates or gets a element-writer to output files.
Ellipse - Class in org.anchoranalysis.mpp.mark.conic
Ellipse() - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipse
Ellipse(Ellipse) - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipse
EllipseBounds - Class in org.anchoranalysis.mpp.bean.mark.bounds
EllipseBounds() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
EllipseBounds(Bound) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
EllipseBounds(EllipseBounds) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
EllipseBoundsCheck - Class in org.anchoranalysis.plugin.mpp.bean.check
EllipseBoundsCheck() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.EllipseBoundsCheck
EllipseBoundsWithoutRotation - Class in org.anchoranalysis.mpp.bean.mark.bounds
EllipseBoundsWithoutRotation() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
EllipseBoundsWithoutRotation(Bound) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
EllipseBoundsWithoutRotation(EllipseBoundsWithoutRotation) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
EllipseStandardFormConverter - Class in org.anchoranalysis.plugin.points.bean.fitter
EllipseStandardFormConverter(DoubleMatrix1D) - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
Ellipsoid - Class in org.anchoranalysis.mpp.mark.conic
Ellipsoid() - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipsoid
Ellipsoid(Ellipsoid) - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipsoid
EllipsoidAxisRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
EllipsoidAxisRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidAxisRatio
EllipsoidBase - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
EllipsoidBase() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
EllipsoidFactory - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
EllipsoidFitHelper - Class in org.anchoranalysis.plugin.points.bean.fitter
Ellipsoidicity - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
Ellipsoidicity() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipsoidicity
EllipsoidMaxAreaIntersectingPlane - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
EllipsoidMaxAreaIntersectingPlane() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidMaxAreaIntersectingPlane
EllipsoidOrientationRadii - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
EllipsoidOrientationRadii() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
EllipsoidUtilities - Class in org.anchoranalysis.mpp.mark.conic
Ellipticity - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
Ellipticity() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipticity
empty() - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates an empty list of features
empty() - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a newly created object-collection that is empty
Empty - Class in org.anchoranalysis.plugin.image.bean.object.provider: Creates an empty object-collection.
Empty() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Empty
EmptyHistogramConstant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Specifies a constant if a histogram is empty, otherwise delegates to another {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
EmptyHistogramConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
enableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta: Assigns additional outputs to enable.
encodeConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
EncodedIntBuffer - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
EncodedIntBuffer(UnsignedIntBuffer, WatershedEncoding) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
encodeDirection(int, int, int) - Method in interface org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodeDirection
encodeDirection(int, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
EncodeDirection - Interface in org.anchoranalysis.plugin.image.segment.watershed.encoding
EncodedVoxels - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
EncodedVoxels(Voxels<UnsignedIntBuffer>) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
ENCODING - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
end() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
end() - Method in class org.anchoranalysis.mpp.feature.bean.mark.CheckMark: Called after any calls to CheckMark.check(org.anchoranalysis.mpp.mark.Mark, org.anchoranalysis.mpp.bean.regionmap.RegionMap, org.anchoranalysis.feature.energy.EnergyStack)
end() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
end() - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
endSeries(NoSharedState, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
endSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
endSeries(OutputSequenceIncrementing<Stack>, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
endSeries(S, U, InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask: Ends processing of a series.
ENERGY_STACK - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
EnergyPair - Class in org.anchoranalysis.mpp.feature.energy
EnergyPair(IdentifiablePair, EnergyTotal) - Constructor for class org.anchoranalysis.mpp.feature.energy.EnergyPair
EnergySavedAll - Class in org.anchoranalysis.mpp.feature.energy.saved
EnergySavedAll() - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
EnergySavedInd - Class in org.anchoranalysis.mpp.feature.energy.saved
EnergySavedInd() - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
EnergySavedPairs - Class in org.anchoranalysis.mpp.feature.energy.saved
EnergySavedPairs(AddCriteria<EnergyPair>) - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
EnergyScheme - Class in org.anchoranalysis.mpp.feature.energy.scheme: The energy for a feature-list as factorized into different cliques.
EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair, Optional<KeyValueParamsProvider>, List<NamedBean<Feature<FeatureInputStack>>>) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
EnergySchemeCreator - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme
EnergySchemeCreator() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreator
EnergySchemeCreatorByElement - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme
EnergySchemeCreatorByElement() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
EnergySchemeSet - Class in org.anchoranalysis.mpp.feature.energy.scheme: A set of EnergySchemes each with a name.
EnergySchemeSet(SharedFeatureMulti) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
EnergySchemeWithSharedFeatures - Class in org.anchoranalysis.mpp.feature.energy.scheme
EnergySchemeWithSharedFeatures(EnergyScheme, SharedFeatureMulti, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
energyStack() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The specified energy stack.
energyStack() - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture
EnergyStack - Class in org.anchoranalysis.feature.energy: An energy-stack with associated KeyValueParams.
EnergyStack(EnergyStackWithoutParams) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
EnergyStack(EnergyStackWithoutParams, KeyValueParams) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
EnergyStack(Channel) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
EnergyStack(Dimensions) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
EnergyStack(Stack) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
EnergyStack(Stack, KeyValueParams) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
EnergyStackWithoutParams - Class in org.anchoranalysis.feature.energy: A stack of channels used as context to calculate features (or calculating energy more broadly).
EnergyStackWithoutParams(Channel) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParams: Create a energy-stack comprised of a single channel
EnergyStackWithoutParams(Dimensions) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParams: Create a energy-stack with no channels - but with dimensions associated
EnergyStackWithoutParams(Stack) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParams: Create a energy-stack comprised of all channels from a stack
EnergyStackWriter - Class in org.anchoranalysis.mpp.io.output: Writes an energy-stack.
EnergyStackWriter(EnergyStack, Outputter) - Constructor for class org.anchoranalysis.mpp.io.output.EnergyStackWriter
EnergyTotal - Class in org.anchoranalysis.feature.energy
EnergyTotal() - Constructor for class org.anchoranalysis.feature.energy.EnergyTotal
EnergyTotal(double) - Constructor for class org.anchoranalysis.feature.energy.EnergyTotal
EnsureRegExMatch - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming: Rejects files that fail to match a particular regular-expression
EnsureRegExMatch() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch
entrySet() - Method in class org.anchoranalysis.core.identifier.name.MapCreate
entrySet() - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
equalMask(BoundingBox, int) - Method in class org.anchoranalysis.image.core.channel.Channel
equals(Object) - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
equals(Object) - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
equals(Object) - Method in class org.anchoranalysis.annotation.io.image.findable.Found
equals(Object) - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
equals(Object) - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization
equals(Object) - Method in class org.anchoranalysis.bean.shared.path.RootPath
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
equals(Object) - Method in class org.anchoranalysis.core.color.RGBColor
equals(Object) - Method in class org.anchoranalysis.core.concurrency.WithPriority
equals(Object) - Method in class org.anchoranalysis.core.graph.TypedEdge
equals(Object) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
equals(Object) - Method in class org.anchoranalysis.core.index.Indexable
equals(Object) - Method in class org.anchoranalysis.core.log.CommonContext
equals(Object) - Method in class org.anchoranalysis.core.system.path.SplitPath
equals(Object) - Method in class org.anchoranalysis.core.value.TypedValue
equals(Object) - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap
equals(Object) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
equals(Object) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
equals(Object) - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputNull
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputResults
equals(Object) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
equals(Object) - Method in class org.anchoranalysis.feature.io.name.CombinedName
equals(Object) - Method in interface org.anchoranalysis.feature.io.name.MultiName: If another name is equal to the current name
equals(Object) - Method in class org.anchoranalysis.feature.io.name.SimpleName
equals(Object) - Method in class org.anchoranalysis.feature.results.ResultsVector
equals(Object) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
equals(Object) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
equals(Object) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
equals(Object) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
equals(Object) - Method in class org.anchoranalysis.image.core.mask.Mask
equals(Object) - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
equals(Object) - Method in class org.anchoranalysis.image.core.object.MatchedObject
equals(Object) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
equals(Object) - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
equals(Object) - Method in class org.anchoranalysis.image.core.stack.Stack
equals(Object) - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
equals(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
equals(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
equals(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
equals(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
equals(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
equals(Object) - Method in class org.anchoranalysis.image.feature.stack.FeatureInputStack
equals(Object) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
equals(Object) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
equals(Object) - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
equals(Object) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
equals(Object) - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
equals(Object) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Checks if two collections are equal in a shallow way
equals(Object) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
equals(Object) - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
equals(Object) - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
equals(Object) - Method in class org.anchoranalysis.io.manifest.file.FileType
equals(Object) - Method in class org.anchoranalysis.io.manifest.ManifestDescription
equals(Object) - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
equals(Object) - Method in class org.anchoranalysis.io.output.outputter.Outputter
equals(Object) - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
equals(Object) - Method in class org.anchoranalysis.launcher.config.HelpConfig
equals(Object) - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
equals(Object) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
equals(Object) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
equals(Object) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
equals(Object) - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
equals(Object) - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
equals(Object) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
equals(Object) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
equals(Object) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
equals(Object) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
equals(Object) - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
equals(Object) - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
equals(Object) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
equals(Object) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
equals(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
equals(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
equals(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
equals(Object) - Method in class org.anchoranalysis.overlay.IndexableOverlays
equals(Object) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
equals(Object) - Method in class org.anchoranalysis.overlay.Overlay
equals(Object) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
equals(Object) - Method in class org.anchoranalysis.plot.AxisLimits
equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
equals(Object) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
equals(Object) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
equals(Object) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
equals(Object) - Method in class org.anchoranalysis.spatial.box.BoundingBox
equals(Object) - Method in class org.anchoranalysis.spatial.Extent
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2d
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2f
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2i
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3d
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3f
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3i
equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3d
equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3f
equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3i
equals(Object) - Method in class org.anchoranalysis.spatial.point.Vector3d
equals(Object) - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
equals(Object...) - Method in class org.anchoranalysis.feature.results.ResultsVector
equals(Dimensions, boolean) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Checks equality betwen this object and another Dimensions, maybe not comparing image-resolution.
equalsDeep(Channel, boolean) - Method in class org.anchoranalysis.image.core.channel.Channel: Are the two channels equal using a deep voxel by voxel comparison?
equalsDeep(Seed) - Method in interface org.anchoranalysis.image.core.object.seed.Seed
equalsDeep(Seed) - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
equalsDeep(Stack, boolean) - Method in class org.anchoranalysis.image.core.stack.Stack: Are the two stack equal using a deep voxel by voxel comparison of each channel?
equalsDeep(BoundedVoxels<?>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
equalsDeep(ObjectCollection) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Checks if two collections are equal in a deeper way
equalsDeep(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
equalsDeep(Voxels<?>) - Method in class org.anchoranalysis.image.voxel.Voxels: Are the voxels identical to another voxels (deep equals)?
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.Mark
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
equalsDeep(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
equalsID(Object) - Method in class org.anchoranalysis.mpp.mark.Mark
equalsIgnoreZ(Object) - Method in class org.anchoranalysis.spatial.Extent: Checks for equality with another extent ignoring any differences in the Z dimension
equalsPrecision(double, Object...) - Method in class org.anchoranalysis.feature.results.ResultsVector
EqualTo - Class in org.anchoranalysis.math.relation
EqualTo() - Constructor for class org.anchoranalysis.math.relation.EqualTo
EqualToBean - Class in org.anchoranalysis.bean.shared.relation
EqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.EqualToBean
equalToPrimitive(Voxels<UnsignedByteBuffer>, byte, ScalarThreeDimensionalConsumer) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: Iterates through all points with a specific voxel intensity-value, passing coordinates as primitive types.
equalToPrimitiveSlice(Voxels<UnsignedByteBuffer>, int, byte, ScalarThreeDimensionalConsumer) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: Like IterateVoxelsEqualTo.equalToPrimitive(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>, byte, org.anchoranalysis.spatial.point.consumer.ScalarThreeDimensionalConsumer) but only iterates over one specific z-slice.
equalToReusePoint(Voxels<UnsignedByteBuffer>, byte, Consumer<Point3i>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: Iterates all points with a specific voxel intensity-value, reusing the Point3i in each iteration.
erode(BinaryVoxels<UnsignedByteBuffer>, boolean, int, Optional<Voxels<UnsignedByteBuffer>>, int, boolean, Optional<AcceptIterationConditon>) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion: Performs a morphological erosion by dilating an inverted version of the object
Erode - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Performs an erosion morphological operation on a binary-image
Erode - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological: Erodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
Erode - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
Erode() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
Erode() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
Erode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
ErosionKernel3 - Class in org.anchoranalysis.image.voxel.kernel.dilateerode: Erosion with a 3x3 or 3x3x3 kernel
ErosionKernel3(BinaryValuesByte, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.ErosionKernel3
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
ErrorNode - Class in org.anchoranalysis.mpp.proposer.error
ErrorNode() - Constructor for class org.anchoranalysis.mpp.proposer.error.ErrorNode
ErrorNodeException - Exception in org.anchoranalysis.mpp.proposer.error
ErrorNodeException(Exception) - Constructor for exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException
ErrorNodeException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException
ErrorNodeImpl - Class in org.anchoranalysis.mpp.proposer.error
ErrorNodeNull - Class in org.anchoranalysis.mpp.proposer.error: Singleton that does nothing with errors
errorReporter() - Method in class org.anchoranalysis.core.log.Logger: Where errors are reported to
ErrorReporter - Interface in org.anchoranalysis.core.log.error
ErrorReporterForTask - Class in org.anchoranalysis.experiment.task: An error-reporter that replaces particular errors/exceptions with user-friendly messages.
ErrorReporterForTask(MessageLogger) - Constructor for class org.anchoranalysis.experiment.task.ErrorReporterForTask
ErrorReporterIntoLog - Class in org.anchoranalysis.core.log.error: Records errors, by writing them into a logger.
ErrorReporterIntoLog(MessageLogger) - Constructor for class org.anchoranalysis.core.log.error.ErrorReporterIntoLog
evalPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.Mark
exchange(int, EnergyTotal) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
exchange(int, Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
exchange(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
exchange(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
exchange(int, VoxelizedMarkMemo, EnergyStack) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
exchange(EnergySavedInd, int, VoxelizedMarkMemo, EnergyStackWithoutParams, EnergySchemeWithSharedFeatures) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
exchange(MemoCollection, int, VoxelizedMarkMemo, EnergyStack) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
exchangeOnUpdatablePairList(ListUpdatableMarkSetCollection, Mark, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
Exclude<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Excludes all inputs that match a regular expression
Exclude() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Exclude
excuteOrWait(CheckedFunction<T, S, ConcurrentModelException>) - Method in class org.anchoranalysis.core.concurrency.ConcurrentModelPool: Execute on the next available model (or wait until one becomes available)
execExperiment(String, String) - Static method in class org.anchoranalysis.test.experiment.launcher.UnitTestCompareUtilities: As we use a common format for storing our tests for the different modules.
execExperimentInTemporary(String, String, boolean, TemporaryFolder) - Static method in class org.anchoranalysis.test.experiment.launcher.UnitTestCompareUtilities: As we use a common format for storing our tests for the different modules.
execute() - Method in interface org.anchoranalysis.io.output.writer.WriterExecuteBeforeEveryOperation: Is called before every operation
execute() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Execute the algorithm.
execute(FeatureInputPairObjects) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
execute(FeatureInputSingleObject, Integer) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: The job processor is expected to remove items from the inputs-list as they are consumed so as to allow garbage-collection of these items before all jobs are processed (as the list might be quite large).
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.SequentialProcessor
execute(FeatureInputAllMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
execute(FeatureInputAllMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
execute(T) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation: This performs the actual calculation when needed.
execute(T) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
execute(T, U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
executeAndAssertCount(int, int, CheckedRunnable<OperationFailedException>) - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture: Executes an operation, and afterwards asserts an expected number of times certain internal methods are called on a mock-calculation.
executeEachWithMonitor(String, List<T>) - Method in class org.anchoranalysis.experiment.task.processor.MonitoredSequentialExecutor: Executes code for each element of inputs in serial, providing log-reports as to how many are finished, remain etc.
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.experiment.bean.Experiment
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Executes the experiment for given arguments.
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
executeExperiment(ExperimentExecutionArguments, boolean, MessageLogger) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: Executes an experiment after finding a single experiment XML file, and reading the experiment from this file
executeExperimentWithParams(ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
executeExperimentWithParams(ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Executes the experiment for parameters.
executeJob(ParametersUnbound<T, S>) - Method in class org.anchoranalysis.experiment.bean.task.Task: Runs the task on one particular input (a job).
executeLogStats(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: Executes the tasks, gathers statistics, and logs them
executePhase() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Execute a single phase of the algorithm.
executingTasks() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
exists() - Method in interface org.anchoranalysis.io.manifest.finder.Finder
exists() - Method in class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
exists() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
exists() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
existsWith(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection: Does this bounding box intersect with another?
existsWithAny(List<BoundingBox>) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection: Does this bounding box intersection with any of the others in the list?
Experiment - Class in org.anchoranalysis.experiment.bean
Experiment() - Constructor for class org.anchoranalysis.experiment.bean.Experiment
ExperimentExecutionArguments - Class in org.anchoranalysis.experiment
ExperimentExecutionArguments() - Constructor for class org.anchoranalysis.experiment.ExperimentExecutionArguments
ExperimentExecutionArguments(Path) - Constructor for class org.anchoranalysis.experiment.ExperimentExecutionArguments
ExperimentExecutionException - Exception in org.anchoranalysis.experiment: An exception that occurs when an experiment is executed.
ExperimentExecutionException(String) - Constructor for exception org.anchoranalysis.experiment.ExperimentExecutionException
ExperimentExecutionException(String, Throwable) - Constructor for exception org.anchoranalysis.experiment.ExperimentExecutionException: A string message displayed to the user as well as a stack-trace of the cause
ExperimentExecutionException(Throwable) - Constructor for exception org.anchoranalysis.experiment.ExperimentExecutionException
ExperimentExecutor - Class in org.anchoranalysis.launcher.executor: Determines where the files passed the ExperimentExecutor are loaded from.
ExperimentExecutorFactory - Class in org.anchoranalysis.launcher.executor
ExperimentFactory - Class in org.anchoranalysis.launcher.executor.selectparam.experiment: SelectParam<Path> factory for experiments.
ExperimentIdentifier - Class in org.anchoranalysis.experiment.bean.identifier
ExperimentIdentifier() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifier
ExperimentIdentifierAuto - Class in org.anchoranalysis.experiment.bean.identifier: Automatically populates a experiment-name and version number
ExperimentIdentifierAuto() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
ExperimentIdentifierConstant - Class in org.anchoranalysis.experiment.bean.identifier: Defines constants for name and version of an experiment
ExperimentIdentifierConstant() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
ExperimentIdentifierConstant(String, String) - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
ExperimentLauncherFromShell - Class in org.anchoranalysis.test.experiment.launcher: Launches an experiment by calling the application 'anchor' via the shell.
ExperimentLauncherFromShell(TestLoader) - Constructor for class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell
ExperimentResultsExperimentStructure - Class in org.anchoranalysis.plugin.quick.bean.structure: Finds some files produced in a previous experiment assuming a certain structure
ExperimentResultsExperimentStructure() - Constructor for class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
experimentSelectParam(CommandLine, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Can point to either: a path ending in .xml, assumed to BeanXML for an experiment nothing, then default experiment is used
ExperimentState - Interface in org.anchoranalysis.mpp.segment.bean
ExperimentStructure - Class in org.anchoranalysis.plugin.quick.bean.structure: A file path prefixer that combines a prefix with an experimentType
ExperimentStructure() - Constructor for class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
ExportFeatureResultsAdder - Interface in org.anchoranalysis.plugin.image.task.feature: Adds results (a row in a feature-table) for export-features
ExportFeatures<T extends InputFromManager,S,U extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature: Calculates features and exports them as a CSV
ExportFeatures() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
ExportImageHistograms - Class in org.anchoranalysis.plugin.image.task.bean.grouped.histogram: Exports a histogram of voxel intensities as a CSV file for each channel of an image.
ExportImageHistograms() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
ExportObjectsAsCroppedImages - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects: Exports a cropped image for each object-mask showing its context within an image
ExportObjectsAsCroppedImages() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
ExportObjectsBase<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
ExportObjectsBase() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
ExportObjectsFromCSV - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects: Given a CSV with a point representing an object-mask, the object-masks are extracted from a segmentation
ExportObjectsFromCSV() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
ExportReportFeatures - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
ExportReportFeatures() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
ExportReportFeaturesFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
ExportReportFeaturesFromManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
ExtendInZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Creates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.
ExtendInZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZ
ExtendInZWithinContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Extends an object (2D/3D) as much as it can within the z-slices of a containing object
ExtendInZWithinContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZWithinContainer
extendWith(int) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2: Switches to extend constant-value out-of-bounds strategy
ExtensionCount - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Remembers each unique extension, and associated count
ExtensionCount() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.SerializedGenerator: Appended to the standard "serialized" extension, to form the complete extension
extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.XStreamGenerator
extent - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent
extent() - Method in class org.anchoranalysis.feature.energy.EnergyStack
extent() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
extent() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
extent() - Method in class org.anchoranalysis.image.core.channel.Channel
extent() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: The width and height and depth of the image i.e.
extent() - Method in class org.anchoranalysis.image.core.mask.Mask
extent() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
extent() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
extent() - Method in class org.anchoranalysis.image.core.stack.Stack
extent() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
extent() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
extent() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
extent() - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
extent() - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
extent() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
extent() - Method in class org.anchoranalysis.image.voxel.Voxels
extent() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
extent() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
extent() - Method in class org.anchoranalysis.spatial.box.BoundingBox: Dimensions in pixels needed to represent the bounding box
Extent<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Width/height/depth of energy-stack in pixels depending on axis
Extent - Class in org.anchoranalysis.spatial: Width, height etc.
Extent() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Extent
Extent(int, int) - Constructor for class org.anchoranalysis.spatial.Extent: Creates with with only x and y dimensions (z dimension is assumed to be 1)
Extent(int, int, int) - Constructor for class org.anchoranalysis.spatial.Extent: Creates with x and y and z dimensions
ExtentMatchHelper - Class in org.anchoranalysis.image.voxel
extract() - Method in class org.anchoranalysis.image.core.channel.Channel
extract() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
extract() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Extracts value from voxels using global coordinates
extract() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
extract() - Method in class org.anchoranalysis.image.voxel.Voxels: Methods to read/copy/duplicate the voxel-values
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsAsFloat
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsAsInt
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsAsShort
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
extract(S) - Method in class org.anchoranalysis.bean.initializable.property.ExtractFromParam
ExtractCenterSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Extracts the slice at the center (rounding down) of the range of z-stacks.
ExtractCenterSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractCenterSlice
extractChannel(String, boolean) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
extractChannel(String, boolean, int) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
extractChannel(Stack, boolean, int) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
ExtractDescriptiveName<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
ExtractDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveName
ExtractDescriptiveNameAndPath<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
ExtractDescriptiveNameAndPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveNameAndPath
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveName
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveNameAndPath
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
ExtractFromParam<S,T> - Class in org.anchoranalysis.bean.initializable.property: Extracts on type of parameter from another
ExtractFromParam(Class<?>, Function<S, T>) - Constructor for class org.anchoranalysis.bean.initializable.property.ExtractFromParam: Constructor
ExtractFromParam(Class<?>, Function<S, T>, Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.ExtractFromParam: Constructor
extractFromVoxelized(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
extractFromVoxelized(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
extractFromVoxelized(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
extractKey(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
extractKey(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
extractKey(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannelsSimple
extractObjectForSummary(T) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
extractObjectForSummary(T) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
extractParamsAsDouble(KeyValueParams, String) - Static method in class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
ExtractPath<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
ExtractPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath
extractScore(VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromVoxelizedMarksWithEnergy
extractScore(DualVoxelizedMarks) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromDualVoxelizedMarks
extractScore(ToPixelized<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.ToPixelizedExtracter
extractScore(T) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.ExtractScoreSize
ExtractScoreSize<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization
ExtractScoreSize() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.ExtractScoreSize
extractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
extractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
extractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
extractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
extractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
extractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
extractSize(VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromVoxelizedMarksWithEnergy
extractSize(DualVoxelizedMarks) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromDualVoxelizedMarks
extractSize(ToPixelized<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.ToPixelizedExtracter
extractSize(T) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.ExtractScoreSize
extractSlice(int) - Method in class org.anchoranalysis.feature.energy.EnergyStack
extractSlice(int) - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
extractSlice(int) - Method in class org.anchoranalysis.image.core.channel.Channel: Creates a new channel contain only of a particular slice (reusing the voxel buffers)
extractSlice(int) - Method in class org.anchoranalysis.image.core.mask.Mask
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.Stack
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
extractSlice(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
extractSlice(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Extracts a particular slice.
extractSlice(int, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Extracts one particular slice as an object-mask
ExtractSlice - Class in org.anchoranalysis.plugin.image.task.bean.slice: Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice
ExtractSlice() - Constructor for class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
ExtractSliceRange - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Extracts slices from sliceStart (inclusive) to sliceEnd (inclusive)
ExtractSliceRange() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
extractStack(ProvidesStackInput, StackProvider, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorRepeated
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxExtentAlongAxis
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMaximumAlongAxis
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMinimumAlongAxis
extractUpToThreeChannels() - Method in class org.anchoranalysis.image.core.stack.Stack
extractValuesFromLeft(long) - Method in class org.anchoranalysis.math.histogram.Histogram
extractValuesFromRight(long) - Method in class org.anchoranalysis.math.histogram.Histogram
ExtractWeightFromMark - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
ExtractWeightFromMark() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ExtractWeightFromMark

F

factory() - Method in class org.anchoranalysis.image.voxel.Voxels
factoryParamsOnly() - Static method in class org.anchoranalysis.feature.list.NamedFeatureStoreFactory
FailureOnlyMessageLogger - Class in org.anchoranalysis.experiment.log: Writes text to a file, but only if FailureOnlyMessageLogger.close(boolean) is called with successful==true.
FailureOnlyMessageLogger(String, OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
Feature<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean: Feature that calculates a result (double) for some parameters
Feature() - Constructor for class org.anchoranalysis.feature.bean.Feature
Feature(PropertyInitializer<FeatureInitParams>) - Constructor for class org.anchoranalysis.feature.bean.Feature
FeatureAllMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
FeatureAllMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureAllMemo
FeatureAsIndividualProportionate - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair: Calculates each feature individually, and combines them using the ratios between itemProportionate as weights
FeatureAsIndividualProportionate() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
FeatureCalculation<S,T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate: Caches the result of a feature, until FeatureCalculation.invalidate() is called.
FeatureCalculation() - Constructor for class org.anchoranalysis.feature.calculate.FeatureCalculation
FeatureCalculationException - Exception in org.anchoranalysis.feature.calculate
FeatureCalculationException(String) - Constructor for exception org.anchoranalysis.feature.calculate.FeatureCalculationException
FeatureCalculationException(String, Throwable) - Constructor for exception org.anchoranalysis.feature.calculate.FeatureCalculationException
FeatureCalculationException(Throwable) - Constructor for exception org.anchoranalysis.feature.calculate.FeatureCalculationException
FeatureCalculationMap<S,T extends FeatureInput,U,E extends Exception> - Class in org.anchoranalysis.feature.calculate: Similar to a FeatureCalculation but stores several evaluations parameterised by a key.
FeatureCalculationMap(int) - Constructor for class org.anchoranalysis.feature.calculate.FeatureCalculationMap: Creates for a particular cache-size.
FeatureCalculatorCachedMulti<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator.cached: A FeatureCalculatorMulti but calculations are cached to avoid repetition if equal FeatureInput are passed.
FeatureCalculatorCachedMulti(FeatureCalculatorMulti<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti: Creates a feature-calculator with a new cache
FeatureCalculatorCachedMulti(FeatureCalculatorMulti<T>, int) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti: Creates a feature-calculator with a new cache
FeatureCalculatorCachedSingle<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator.cached: A FeatureCalculatorSingle but calculations are cached to avoid repetition if equal FeatureInput are passed.
FeatureCalculatorCachedSingle(FeatureCalculatorSingle<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle: Creates a feature-calculator with a new cache
FeatureCalculatorCachedSingle(FeatureCalculatorSingle<T>, int) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle: Creates a feature-calculator with a new cache
FeatureCalculatorFromProvider<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.task.feature.calculator: Calculates feature or feature values.
FeatureCalculatorFromProvider(ProvidesStackInput, Optional<StackProvider>, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider
FeatureCalculatorMulti<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.calculator: Calculates one or more features for given params
FeatureCalculatorMultiChangeInput<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator: Likes a SequentialSession but automatically changes parameters before calculation
FeatureCalculatorMultiChangeInput(FeatureCalculatorMulti<T>, Consumer<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput: Constructor
FeatureCalculatorMultiFromSingle<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator
FeatureCalculatorMultiFromSingle(FeatureCalculatorSingle<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
FeatureCalculatorMultiReuse<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator: Remembers the first-calculation and always returns this value for all subsequent calculations
FeatureCalculatorMultiReuse(FeatureCalculatorMulti<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
FeatureCalculatorRepeated - Class in org.anchoranalysis.plugin.image.task.feature.calculator
FeatureCalculatorSingle<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.calculator: Calculates the result of a feature for particular params
FeatureCalculatorSingleChangeInput<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator: Likes a SequentialSession but automatically changes parameters before calculation
FeatureCalculatorSingleChangeInput(FeatureCalculatorSingle<T>, Consumer<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleChangeInput
FeatureCalculatorSingleFromMulti<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator: Exposes a FeatureCalculatorMulti as a FeatureCalculatorSingle
FeatureCalculatorSingleFromMulti(FeatureCalculatorMulti<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleFromMulti
FeatureConvertUnits<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
FeatureConvertUnits() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
FeatureConvertUnits(Feature<T>, SpatialUnits.UnitSuffix) - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
FeatureCostAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
FeatureCostAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
FeatureCSVMetadata - Class in org.anchoranalysis.feature.io.csv: What's needed to output a CSV other than the actual data items.
FeatureCSVMetadata(String, List<String>) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
FeatureCSVWriter - Class in org.anchoranalysis.feature.io.csv: Writes the results of feature-calculations as a CSV file.
FeatureCSVWriter(CSVWriter) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureCSVWriter
FeatureDeriveFromPair - Class in org.anchoranalysis.image.feature.bean.object.pair: Base class for evaluating FeaturePairObjects in terms of another feature that operations on elements (first, second, merged etc.)
FeatureDeriveFromPair() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
FeatureDeriveFromPair(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromManifest
featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromPath
featureDescription(T, Logger) - Method in class org.anchoranalysis.io.output.bean.ReportFeature
FeatureDoubleElem<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
FeatureDoubleElem() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
FeatureEnergy<T extends FeatureInputEnergy> - Class in org.anchoranalysis.image.feature.bean: A base class for features that only require an input that extends from FeatureInputEnergy
FeatureEnergy() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureEnergy
FeatureEnergyChannel - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: A feature that uses a channel from the energy-stack as identified by an index
FeatureEnergyChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
FeatureEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.bean.evaluator: Defines a feature and provides a means to calculate inputs for it, a session.
FeatureEvaluator() - Constructor for class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
FeatureHistogram - Class in org.anchoranalysis.image.feature.bean
FeatureHistogram() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureHistogram
FeatureHistogramStatistic - Class in org.anchoranalysis.image.feature.histogram
FeatureHistogramStatistic() - Constructor for class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
FeatureInitParams - Class in org.anchoranalysis.feature.calculate: Parameters used to initialize a feature before any calculations
FeatureInitParams() - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
FeatureInitParams(Optional<KeyValueParams>, Optional<EnergyStackWithoutParams>, Optional<SharedObjects>) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
FeatureInitParams(SharedObjects) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
FeatureInitParams(KeyValueParams) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
FeatureInitParams(EnergyStack) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
FeatureInput - Interface in org.anchoranalysis.feature.input: A single input used for feature-calculation to produce a result.
FeatureInputAllMemo - Class in org.anchoranalysis.mpp.feature.input.memo
FeatureInputAllMemo(MemoCollection, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
FeatureInputEnergy - Class in org.anchoranalysis.feature.input
FeatureInputEnergy() - Constructor for class org.anchoranalysis.feature.input.FeatureInputEnergy
FeatureInputEnergy(Optional<EnergyStack>) - Constructor for class org.anchoranalysis.feature.input.FeatureInputEnergy
FeatureInputHistogram - Class in org.anchoranalysis.image.feature.histogram
FeatureInputHistogram(Histogram, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.feature.histogram.FeatureInputHistogram
FeatureInputMark - Class in org.anchoranalysis.mpp.feature.bean.mark
FeatureInputMark(Mark, Optional<Dimensions>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
FeatureInputMark(Mark, Optional<Dimensions>, Optional<KeyValueParams>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
FeatureInputMark(Mark, Dimensions, KeyValueParams) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
FeatureInputMarkCollection - Class in org.anchoranalysis.mpp.feature.bean.mark.collection
FeatureInputMarkCollection(MarkCollection, Optional<Dimensions>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
FeatureInputNull - Class in org.anchoranalysis.feature.input
FeatureInputObjectCollection - Class in org.anchoranalysis.image.feature.object.input
FeatureInputObjectCollection(ObjectCollection) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
FeatureInputObjectCollection(ObjectCollection, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
FeatureInputOverlappingCircleFixture - Class in org.anchoranalysis.test.feature.plugins.objects
FeatureInputPairMemo - Class in org.anchoranalysis.mpp.feature.input.memo
FeatureInputPairMemo(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
FeatureInputPairObjects - Class in org.anchoranalysis.image.feature.object.input: A pair of objects (first and second) and maybe a merged version of both
FeatureInputPairObjects(FeatureInputPairObjects) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
FeatureInputPairObjects(ObjectMask, ObjectMask) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>, Optional<ObjectMask>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
FeatureInputPairObjects(ObjectMask, ObjectMask, EnergyStack) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
FeatureInputParams - Interface in org.anchoranalysis.feature.input: A feature-input that is associated with particular key-value parameters
FeatureInputResults - Class in org.anchoranalysis.feature.input
FeatureInputResults(ResultsVectorList, FeatureNameMapToIndex) - Constructor for class org.anchoranalysis.feature.input.FeatureInputResults
FeatureInputSingleMemo - Class in org.anchoranalysis.mpp.feature.input.memo
FeatureInputSingleMemo(VoxelizedMarkMemo, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
FeatureInputSingleMemo(VoxelizedMarkMemo, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
FeatureInputSingleObject - Class in org.anchoranalysis.image.feature.object.input: An input representing a single object-mask (with maybe an energy-stack associated)
FeatureInputSingleObject(ObjectMask) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
FeatureInputSingleObject(ObjectMask, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
FeatureInputSingleObject(ObjectMask, EnergyStack) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
FeatureInputStack - Class in org.anchoranalysis.image.feature.stack
FeatureInputStack() - Constructor for class org.anchoranalysis.image.feature.stack.FeatureInputStack: Should only be used if it's guaranteed the energy stack will be added later, as this this required.
FeatureInputStack(Optional<EnergyStackWithoutParams>) - Constructor for class org.anchoranalysis.image.feature.stack.FeatureInputStack: Params without any ImageInitParams
FeatureInputStack(EnergyStackWithoutParams) - Constructor for class org.anchoranalysis.image.feature.stack.FeatureInputStack: Params without any ImageInitParams
FeatureInputType - Class in org.anchoranalysis.feature.input: Performs checks and aggregations on feature-input types are compatible with others
FeatureInputWithResolution - Interface in org.anchoranalysis.feature.input
FeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
FeatureIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
FeatureIntersectingObjectsSingleElement - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
FeatureIntersectingObjectsSingleElement() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
FeatureIntersectingObjectsThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
FeatureIntersectingObjectsThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold
FeatureList<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list: A list of features with the same input-type.
FeatureList() - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Standard Bean Constructor.
FeatureList(List<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Wraps an existing list
FeatureList(Stream<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Creates a list from a stream
FeatureListCSVGeneratorHorizontal - Class in org.anchoranalysis.feature.io.csv: CSV file where each feature is a column (spanning horizontally).
FeatureListCSVGeneratorHorizontal(String, FeatureNameList) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorHorizontal: Creates without setting any results (i.e.
FeatureListCSVGeneratorVertical - Class in org.anchoranalysis.feature.io.csv: CSV file where each feature is a row (spanning vertically).
FeatureListCSVGeneratorVertical(String, FeatureNameList) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorVertical: Creates without setting any results (i.e.
FeatureListElem<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
FeatureListElem() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureListElem
FeatureListElem(FeatureList<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureListElem: Constructor
FeatureListEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.bean.evaluator: Defines a list of features and provides a means to calculate inputs for it, a session.
FeatureListEvaluator() - Constructor for class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator
FeatureListFactory - Class in org.anchoranalysis.feature.bean.list: Factory for creating FeatureList in different ways
FeatureListProvider<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
FeatureListProvider() - Constructor for class org.anchoranalysis.feature.bean.list.FeatureListProvider
FeatureListProviderAggregatePair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates features on each part of a pair (first, second, merged etc.) and then reduces the calculation to a single number.
FeatureListProviderAggregatePair() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
FeatureListProviderLDAClassifier<T extends FeatureInput> - Class in org.anchoranalysis.plugin.ml.bean.classifier
FeatureListProviderLDAClassifier() - Constructor for class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
FeatureListProviderSVMClassifier - Class in org.anchoranalysis.plugin.ml.bean.classifier
FeatureListProviderSVMClassifier() - Constructor for class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
FeatureListStoreUtilities - Class in org.anchoranalysis.feature.list
FeatureMark - Class in org.anchoranalysis.mpp.feature.bean.mark
FeatureMark() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureMark
FeatureMarkCollection - Class in org.anchoranalysis.mpp.feature.bean.mark.collection
FeatureMarkCollection() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
FeatureMarkDirection - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
FeatureMarkDirection() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
FeatureMarkEccentricity - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
FeatureMarkEccentricity() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity
FeatureMarkRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
FeatureMarkRegion() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.FeatureMarkRegion
FeatureNameList - Class in org.anchoranalysis.feature.name: A list of Strings representing feature names
FeatureNameList() - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
FeatureNameList(String) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
FeatureNameList(Set<String>) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
FeatureNameList(Stream<String>) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
FeatureNameMapToIndex - Class in org.anchoranalysis.feature.name: A map of Feature-Names (Strings) to indexes (Int)
FeatureNameMapToIndex() - Constructor for class org.anchoranalysis.feature.name.FeatureNameMapToIndex
featureNamesNonAggregate() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata: Names of each feature in the feature columns.
FeatureObjectCollection - Class in org.anchoranalysis.image.feature.bean.object.collection
FeatureObjectCollection() - Constructor for class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
FeatureOperator<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator: Base class for features that broadly accept any type of feature-input.
FeatureOperator() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureOperator
FeaturePairMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
FeaturePairMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeaturePairMemo
FeaturePairMemoOne - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
FeaturePairMemoOne() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoOne
FeaturePairMemoSingleRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
FeaturePairMemoSingleRegion() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
FeaturePairObjects - Class in org.anchoranalysis.image.feature.bean.object.pair
FeaturePairObjects() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeaturePairObjects
FeatureProvider<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.provider
FeatureProvider() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProvider
FeatureProviderBean<B,P> - Class in org.anchoranalysis.feature.bean.provider
FeatureProviderBean() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderBean
FeatureProviderDefine<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.provider
FeatureProviderDefine() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
FeatureProviderDefine(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
FeatureProviderReference - Class in org.anchoranalysis.feature.bean.provider
FeatureProviderReference() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
FeatureRelatedBean<T> - Class in org.anchoranalysis.feature.bean: Beans-related to features that require initialization with SharedFeaturesInitParams
FeatureRelatedBean() - Constructor for class org.anchoranalysis.feature.bean.FeatureRelatedBean
FeatureResults - Class in org.anchoranalysis.feature.bean.results: Features that process ResultsVectorList.
FeatureResults() - Constructor for class org.anchoranalysis.feature.bean.results.FeatureResults
FeatureResultSupplier - Interface in org.anchoranalysis.plugin.operator.feature.score: Supplies the result of a feature-calculation
features() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
FeatureSession - Class in org.anchoranalysis.feature.session: A single-point in the code for creating feature-sessions (a factory).
FeatureSessionCache<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache: A context in which to calculate features while caching certain duplicated internal calculations among the features.
FeatureSessionCacheFactory - Interface in org.anchoranalysis.feature.session.cache
FeatureSessionCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache: Calculates features in the context of a particular feature-session.
FeaturesFromXmlFixture - Class in org.anchoranalysis.test.feature.plugins
FeatureSingleMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
FeatureSingleMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
FeatureSingleMemoRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
FeatureSingleMemoRegion() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
FeatureSingleObject - Class in org.anchoranalysis.image.feature.bean.object.single
FeatureSingleObject() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject
FeatureSingleObjectFromShared<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates as object-masks from entities in shared, using the feature-input only for a energy-stack.
FeatureSingleObjectFromShared() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
FeatureSource<T extends InputFromManager,S,U extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Extracts features from some kind of inputs to produce one or more rows in a feature-table.
FeatureSource() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
FeatureStack - Class in org.anchoranalysis.image.feature.bean.stack
FeatureStack() - Constructor for class org.anchoranalysis.image.feature.bean.stack.FeatureStack
FeatureSymbolCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache: Resolves and calculates a feature by a symbol (an ID/variable-name referring to another feature)
FeatureTableCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.image.feature.session: A feature-calculator with additional functions for encoding the output in in a tabular-format with column-names
FeatureTableCSVGenerator<T> - Class in org.anchoranalysis.feature.io.csv: Base class for a Generator that outputs a feature-table in CSV format.
FeatureTableCSVGenerator(String, List<String>) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureTableCSVGenerator: Creates for a particular manifest-function and headers.
FeatureTestCalculator - Class in org.anchoranalysis.test.feature.plugins
FeatureTestCalculatorDuo - Class in org.anchoranalysis.test.feature.plugins: Tests that consider two possibilities: positive and negative
featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Which feature to calculate the input-value? The result is then passed to RangeCompareBase.calculateForValue(double, org.anchoranalysis.feature.calculate.cache.SessionInput<T>)
FeatureUnary<T extends FeatureInput,S extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator: A feature that contains another feature as a bean-parameter.
FeatureUnary() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnary
FeatureUnary(Feature<S>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnary
FeatureUnaryGeneric<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator: A FeatureUnary that accepts any {#link FeatureInput} irrespective of type.
FeatureUnaryGeneric() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnaryGeneric
FeatureUnaryGeneric(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnaryGeneric
FeatureValueCheckMark<T extends FeatureInput> - Class in org.anchoranalysis.plugin.mpp.bean.check
FeatureValueCheckMark() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
FeatureValueIndividualEnergyGreaterThan - Class in org.anchoranalysis.plugin.mpp.bean.check
FeatureValueIndividualEnergyGreaterThan() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueIndividualEnergyGreaterThan
FeatureValueMarkGreaterEqualThan - Class in org.anchoranalysis.plugin.mpp.bean.check
FeatureValueMarkGreaterEqualThan() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueMarkGreaterEqualThan
FeedbackBeginParameters<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback
FeedbackBeginParameters() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
FeedbackEndParameters<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback
FeedbackEndParameters(T, MessageLogger) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
FeedbackReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback
FeedbackReceiverBean<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
FeedbackReceiverBean() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverBean
FeedbackReceiverList<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
FeedbackReceiverList() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
FeedbackReceiverRequireArguments<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
FeedbackReceiverRequireArguments() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
fetchUnmatchedWorker() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
fields() - Method in class org.anchoranalysis.bean.AnchorBean: A list of all bean-fields that are associated with this bean directly (fields of children are not checked).
FileDetails - Class in org.anchoranalysis.plugin.io.multifile
FileDetails(Path, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Constructor for class org.anchoranalysis.plugin.io.multifile.FileDetails
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMETiff
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMEXML
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
fileInputManager() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
FileLabelMap<T> - Class in org.anchoranalysis.image.experiment.label
FileLabelMap() - Constructor for class org.anchoranalysis.image.experiment.label.FileLabelMap
FileMatch - Class in org.anchoranalysis.io.manifest.finder.match
filePath() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
FilePath - Class in org.anchoranalysis.plugin.io.bean.filepath
FilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.FilePath
FilePathAppendBase - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
FilePathAppendBase() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
FilePathBaseAppendToManager - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
FilePathBaseAppendToManager() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManager
FilePathBaseAppendToManagerWithFileID - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
FilePathBaseAppendToManagerWithFileID() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManagerWithFileID
FilePathCounter - Class in org.anchoranalysis.io.output.bean.path.prefixer
FilePathCounter() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
FilePathCounter(String) - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
FilePathParser - Class in org.anchoranalysis.plugin.io.bean.groupfiles.parser
FilePathParser() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
FilePathPattern - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Converts a list of file-paths into a form that tries to find a pattern in the naming style using the path-pattern-finder library
FilePathPattern() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
FilePathPrefixerContext - Class in org.anchoranalysis.io.output.path.prefixer
FilePathPrefixerContext(boolean, Optional<Path>) - Constructor for class org.anchoranalysis.io.output.path.prefixer.FilePathPrefixerContext
FilePathResolver - Class in org.anchoranalysis.launcher
FilePathResolver(Class<?>) - Constructor for class org.anchoranalysis.launcher.FilePathResolver
FilePathToUnixStyleConverter - Class in org.anchoranalysis.core.system.path: Conversion to Unix-style separators
FileSetFromStringSet - Class in org.anchoranalysis.plugin.io.bean.provider.file
FileSetFromStringSet() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
FileSizeStatistics - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Tracks the range of file-size.
FileSizeStatistics() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
FileType - Class in org.anchoranalysis.io.manifest.file
FileType(ManifestDescription, String) - Constructor for class org.anchoranalysis.io.manifest.file.FileType
fill(BinaryVoxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.plugin.imagej.mask.ApplyImageJMorphologicalOperation
FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider
FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.object.provider: Fills holes in an object.
FillHoles() - Constructor for class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
FillHoles() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
filter(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Filters a ObjectCollection to include certain items based on a predicate
filter(Stream<T>, Class<? extends Exception>, CheckedPredicate<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a Stream.filter(java.util.function.Predicate<? super T>) but accepts a predicate that can throw a checked-exception
filter(CheckedPredicate<ObjectMask, E>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Filters a ObjectCollection to include certain items based on a predicate - and optionally store rejected objects.
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.object.ObjectFilter: Filters an object-collection to remove objects according to a criteria
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.And
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.Or
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
Filter - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
Filter - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Applies an object-filter to the results of an upstream segmentation.
Filter() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.Filter
Filter() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
filterAndMap(Predicate<Feature<T>>, CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Filters inputs and then performs a FeatureList.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.feature.bean.Feature<T>, org.anchoranalysis.feature.bean.Feature<S>, E>)
filterAndMap(Predicate<ObjectMask>, UnaryOperator<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Performs a ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) and then a ObjectMaskStream.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.image.voxel.object.ObjectMask, org.anchoranalysis.image.voxel.object.ObjectMask, E>).
filterAndMapFrom(Iterable<T>, Predicate<T>, CheckedFunction<T, ObjectWithProperties, E>) - Static method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithPropertiesFactory: Creates a new collection by filtering an iterable and then mapping it to ObjectWithProperties
filterAndMapFrom(Iterable<T>, Predicate<T>, CheckedFunction<T, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by filtering an iterable and then mapping it to ObjectMask
filterAndMapToList(List<S>, Predicate<S>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Creates a new collection by filtering a list and then mapping to a list of another type.
filterAndMapWithIndexFrom(List<T>, Predicate<T>, CheckedBiFunction<T, Integer, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by filtering a list and then mapping from it to ObjectMask.
filterAndMapWithIndexToList(List<S>, Predicate<S>, CheckedBiFunction<S, Integer, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Creates a new collection by filtering a list and then mapping (with an index) to a list of another type.
FilterByGroup - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
FilterByGroup() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
FilterCsvColumn<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Finds a CSV file with the names of an input as the first-column.
FilterCsvColumn() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
FilterDescriptiveName<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Filters all the input objects for only those with certain types of descriptive-names.
FilterDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
FilterDescriptiveNameEqualsContains - Class in org.anchoranalysis.plugin.io.input.filter: Filters a list of input-objects by the descriptive name
FilterDescriptiveNameEqualsContains(String, String) - Constructor for class org.anchoranalysis.plugin.io.input.filter.FilterDescriptiveNameEqualsContains: Constructor
filterExclude(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Filters a ObjectCollection to exclude certain items based on a predicate
FilterForExistingFiles - Class in org.anchoranalysis.plugin.io.bean.input.files.provider
FilterForExistingFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
FilterHelper - Class in org.anchoranalysis.plugin.imagej.channel.provider
FilterIfDebug<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Filters a list of inputs when in debug-mode
FilterIfDebug() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
filterSubset(Predicate<ObjectMask>, List<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Like ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) but only operates on certain indices of the collection.
filterToList(Collection<T>, Class<? extends Exception>, CheckedPredicate<T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Filters a collection and maps the result to a list
filterToList(Collection<T>, Predicate<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Filters a collection and maps the result to a list
finalizeBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
finalizeBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityByteBuffer
finalizeBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityShortBuffer
Findable<T> - Interface in org.anchoranalysis.annotation.io.image.findable: An object that can be Found or NotFound.
findArbitraryOnVoxel() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Finds any arbitrary "ON" voxel on the object.
FindChildStrategy - Interface in org.anchoranalysis.feature.session.strategy.child
findClosestResult(Point3i) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
FindCommonVoxelType - Class in org.anchoranalysis.image.voxel.datatype: Finds a common voxel-data type to represent two types.
findDirectory(List<MutableDirectory>, Predicate<MutableDirectory>) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
Finder - Interface in org.anchoranalysis.io.manifest.finder
FinderExperimentFileDirectories - Class in org.anchoranalysis.io.manifest.finder
FinderExperimentFileDirectories() - Constructor for class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
FinderFileAsText - Class in org.anchoranalysis.io.manifest.finder
FinderFileAsText(String, ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderFileAsText
FinderKeyValueParams - Class in org.anchoranalysis.io.manifest.finder
FinderKeyValueParams(String, ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderKeyValueParams
FinderSerializedObject<T> - Class in org.anchoranalysis.io.manifest.finder
FinderSerializedObject(String, ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderSerializedObject
FinderSingleDirectory - Class in org.anchoranalysis.io.manifest.finder
FinderSingleDirectory() - Constructor for class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
FinderSingleFile - Class in org.anchoranalysis.io.manifest.finder
FinderSingleFile(ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderSingleFile
FinderUtilities - Class in org.anchoranalysis.io.manifest.finder
FindFailedException - Exception in org.anchoranalysis.io.manifest.finder
FindFailedException(String) - Constructor for exception org.anchoranalysis.io.manifest.finder.FindFailedException
FindFailedException(Throwable) - Constructor for exception org.anchoranalysis.io.manifest.finder.FindFailedException
findFieldsOfClass(Class<?>) - Method in class org.anchoranalysis.bean.AnchorBean: Finds all bean-fields that are instances of a certain class.
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.JobRootDirectory
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.Subdirectory
findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderFileAsText
findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderKeyValueParams
findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSerializedObject
findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
findFileFromIndex(List<OutputtedFile>, String, boolean) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
findFileFromIndex(List<OutputtedFile>, String, boolean) - Method in interface org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectory
findIndex(String) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
findListFile(Manifest, Predicate<OutputtedFile>) - Static method in class org.anchoranalysis.io.manifest.finder.FinderUtilities
findListFolder(Manifest, Predicate<MutableDirectory>) - Static method in class org.anchoranalysis.io.manifest.finder.FinderUtilities
findMatch(ObjectCollection) - Method in class org.anchoranalysis.image.bean.object.ObjectMatcher: Finds matches for objects
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection
findMaxPriority() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
FindMinimumDistance - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine: TODO naming is too complicated in functions with lots of min/max
findMostDeepCombinableException() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Traverses through the nested-exceptions and finds the most deep exception that is combinable using the rules about combining and skipping outlined in the class description
findObjectsMatchingRow(ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
findObjectsMatchingRow(CSVRow, ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
findObjectsMatchingRow(CSVRow, ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
findObjectsMatchingRow(CSVRow, ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
findObjectsWithIntersectingBBox(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
findOptimum(KernelProposer<S>, ListUpdatableMarkSetCollection, FeedbackReceiver<S>, OptimizationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
findOptimum(KernelProposer, ListUpdatableMarkSetCollection, FeedbackReceiver<S>, OptimizationContext) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.OptimizationScheme: Finds an optimal state
findOptimum(KernelProposer, ListUpdatableMarkSetCollection, FeedbackReceiver<S>, OptimizationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
FindOutline - Class in org.anchoranalysis.image.core.outline: Finds outline voxels i.e.
FindPointOnOutline - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline: Finds a pixel on the outline of an object in a particular direction
FindPointOnOutline() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutline
FindPointOnOutlineWalk - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline: Walks in a particular direction until the outline is found.
FindPointOnOutlineWalk() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
findRoot(String, boolean) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap: Finds a root to match a name and debug/status
findSingleItem(Manifest, Predicate<OutputtedFile>) - Static method in class org.anchoranalysis.io.manifest.finder.FinderUtilities
first() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: For recording first-level outputs.
first() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
First - Class in org.anchoranalysis.image.feature.bean.object.pair: Evaluates the first-object in a pair only
First() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.First
First(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.First
FIRST - org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
firstConnectedTo(ContourList) - Method in class org.anchoranalysis.plugin.points.contour.ContourList
firstLevelContains(String) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
firstPart() - Method in class org.anchoranalysis.feature.io.name.CombinedName
firstPart() - Method in interface org.anchoranalysis.feature.io.name.MultiName: The first part, and grouping key.
firstPart() - Method in class org.anchoranalysis.feature.io.name.SimpleName
firstPart() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
firstPartWithCustomMiddle(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
firstPartWithDataset() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase: The first-part of the out-path string including the dataset of the current experiment as a folder
firstPartWithFilename() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase: The first-part of the out-path string including the file-name of the previous experiment as a folder
FirstSecondOrderStatistic - Class in org.anchoranalysis.math.statistics
FirstSecondOrderStatistic() - Constructor for class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.mpp.bean.points.fitter.PointsFitter
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
FitBoxToOnVoxels - Class in org.anchoranalysis.plugin.image.bean.mask.provider.resize: Fits a box around the ON pixels.
FitBoxToOnVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
fitMarkToPointsFromMarks(MarkCollection, Dimensions) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Extract points from a marks, creates a new mark from markProvider and then fits this mark the extracted points
FitPoints - Class in org.anchoranalysis.plugin.points.bean.mark.proposer.single
FitPoints() - Constructor for class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
fitPointsToMark(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
FitResult - Class in org.anchoranalysis.plugin.points.bean.fitter
FitResult() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.FitResult
flagForNoRegion() - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
flagForRegion(int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
flagForRegion(int, int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Combines two regions
flagForRegion(int, int, int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Combines three regions
flags() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
flatBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
flatMap(Class<? extends Exception>, CheckedFunction<ObjectMask, ObjectCollection, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Like a typical flatMap() operation but accepts a mapping function that throws a checked exception.
flatMap(Function<ObjectMask, ObjectCollection>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping each item to several others.
flatMap(Optional<S>, CheckedFunction<S, Optional<T>, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Like Optional.flatMap(java.util.function.Function<? super T, ? extends java.util.Optional<? extends U>>) but tolerates an exception in the mapping function, which is immediately thrown.
flatMap(Stream<S>, Class<? extends Exception>, CheckedFunction<S, Collection<? extends T>, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a Stream.flatMap(java.util.function.Function<? super T, ? extends java.util.stream.Stream<? extends R>>) but accepts a function that can throw a checked-exception
flatMapFrom(Collection<T>, Function<T, ObjectCollection>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by flatMapping an incoming stream to ObjectCollection
flatMapFrom(Stream<T>, Class<? extends Exception>, CheckedFunction<T, ObjectCollection, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by flatMapping an incoming stream to ObjectCollection AND rethrowing any exception during mapping
flatMapFromCollection(Stream<T>, Class<? extends Exception>, CheckedFunction<T, Collection<? extends ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new ObjectCollection by flatMapping an incoming stream to Collection<ObjectMask> AND rethrowing any exception during mapping
flatMapFromOptional(Iterable<S>, CheckedFunction<S, Optional<FeatureList<T>>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by flat-mapping an iterable to an optional feature
flatMapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectCollection, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection
flatMapFromRange(int, int, IntFunction<ObjectCollection>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection
flatMapToList(Collection<S>, Function<S, Stream<T>>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Flat-maps a collection to a list where in the original collection can produce many elements in the outging list.
FlattenAsChannel - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Combines all series and frames returned by a reader by converting them into multiple channels in the same image
FlattenAsChannel() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
flattenZ() - Method in class org.anchoranalysis.image.core.mask.Mask
flattenZ() - Method in interface org.anchoranalysis.image.core.object.seed.Seed
flattenZ() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
flattenZ() - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
flattenZ() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A maximum-intensity projection (flattens in z dimension)
flattenZ() - Method in class org.anchoranalysis.spatial.box.BoundingBox
flattenZ() - Method in class org.anchoranalysis.spatial.Extent: Collapses the Z dimension i.e.
FlattenZ - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice: Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
FlattenZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice: Flattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
FlattenZ() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.slice.FlattenZ
FlattenZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.FlattenZ
floatArray(float[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an float-array into a voxel-buffer.
floatBuffer(FloatBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps a float buffer into a voxel-buffer.
floatFromDouble(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
floatFromInt(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
floatFromInt(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
floatFromIntDropZ(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter: Creates a new Point3f with X, Y values from the Point3i but setting Z to be 0
FloatFromUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat
FloatFromUnsignedByte() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
FloatFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat
FloatFromUnsignedInt(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
FloatUtilities - Class in org.anchoranalysis.math.arithmetic: Utilities for arithmetic operations involving type float
FloatVoxelType - Class in org.anchoranalysis.image.voxel.datatype
FloodFillEachIntensityLevel - Class in org.anchoranalysis.plugin.imagej.bean.object.segment: Creates an object for each separate intensity-value (beginning at startingColor) by flood-filling.
FloodFillEachIntensityLevel() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
forBoxes(BoundingBox, BoundingBox) - Static method in class org.anchoranalysis.plugin.image.box.IntersectionOverUnion: Calculates the intersection-over-union score a pair of bounding-boxes.
ForceBitsPerPixel - Class in org.anchoranalysis.io.bioformats.bean.options
ForceBitsPerPixel() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
ForceChannelsPerByteArray - Class in org.anchoranalysis.io.bioformats.bean.options
ForceChannelsPerByteArray() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
ForceNumberChannels - Class in org.anchoranalysis.io.bioformats.bean.options
ForceNumberChannels() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
ForceNumberFrames - Class in org.anchoranalysis.io.bioformats.bean.options
ForceNumberFrames() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
ForceTimeSeriesToStack - Class in org.anchoranalysis.io.bioformats.bean.options: Treats a time-series as if it was a z-stack
ForceTimeSeriesToStack() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
forChild() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput: Performs calculations not on the main cache, but on a child cache
forChild() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
forEach(Stream<T>, Class<? extends Exception>, CheckedConsumer<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a Stream.forEach(java.util.function.Consumer<? super T>) but accepts a consumer that can throw a checked-exception
forEach(CheckedBiConsumer<String, StoreSupplier<Stack>, E>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks: Iterates over each entry in the map.
forList(List<Point3i>) - Static method in class org.anchoranalysis.image.core.points.BoundingBoxFromPoints: Create from a list of points
ForSpecificAxis<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Dimensions-calculation for one specific axis only.
ForSpecificAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
forTwoPoints(Point3d, Point3d) - Static method in class org.anchoranalysis.image.core.points.BoundingBoxFromPoints: Creates a bounding-box for two unordered points.
Found<T> - Class in org.anchoranalysis.annotation.io.image.findable: A positive-result when an object is found.
Found(T) - Constructor for class org.anchoranalysis.annotation.io.image.findable.Found
FrequencyMap<T> - Class in org.anchoranalysis.plugin.io.summarizer: Counts the frequency of certain strings, and describes the contents in human language.
FrequencyMap() - Constructor for class org.anchoranalysis.plugin.io.summarizer.FrequencyMap
friendlyMessage() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
friendlyMessage() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
friendlyMessage() - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage: A friendly message to describe to the user what went wrong.
friendlyMessageHierarchy() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
friendlyMessageHierarchy() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
friendlyMessageHierarchy() - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage: A friendly message to describe to the user what went wrong, which doesn't impose a fixed-size, or showExceptionNames
friendlyMessageHierarchy(Writer, int, boolean) - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
friendlyMessageHierarchy(Writer, int, boolean) - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
friendlyMessageHierarchy(Writer, int, boolean) - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage: A friendly message to describe to the user what went wrong, including all nested exceptions that have a non-empty error message
from(Feature<T>...) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list for one or more features
from(Channel) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus: Creates an ImagePlus from a Channel.
from(Stack, boolean) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus: Creates an ImagePlus from a Stack.
from(VoxelsWrapper) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Converts from a VoxelsWrapper (Anchor structure) to a Img (ImgLib2 structure).
from(VoxelsWrapper) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus: Creates an ImagePlus from a VoxelsWrapper.
from(VoxelsWrapper, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor: Creates a ImageProcessor by extracting a slice from a VoxelsWrapper.
FromAnnotations<T extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.file
FromAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
fromByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
fromByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor: Creates a ImageProcessor from voxel-buffer (of type ByteBuffer) that is already a slice.
fromByte(SliceBufferIndex<UnsignedByteBuffer>, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor: Creates a ImageProcessor by extracting a slice from a SliceBufferIndex of type UnsignedByteBuffer.
fromByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
fromByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg
FromByte - Class in org.anchoranalysis.image.voxel.factory.sliceindex
FromChannel - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider: Creates image-dimensions by referencing them from a ChannelProvider
FromChannel - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
FromChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert: Creates a mask from an existing channel, reusing the channel's buffer and considering all 0 values as OFF, and 255 values as ON
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromChannel
FromChannelBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Base-class for mask-providers that accept a channel as input
FromChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
FromChannelOrMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Creates a stack from a channel or mask (reusing the voxel buffers)
FromChannelOrMask() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
FromChannelOrMask(ChannelProvider) - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
FromCSVInput - Class in org.anchoranalysis.plugin.mpp.experiment.objects
FromCSVInput(MultiInput, Path) - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
FromCSVInputManager - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
FromCSVInputManager() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
FromCSVSharedState - Class in org.anchoranalysis.plugin.mpp.experiment.objects: Shared-state for ExportObjectsFromCSV
FromCSVSharedState() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVSharedState
FromDescriptiveName - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer: The prefixer uses a combination of a out-path-prefix and the descriptive-name of inputs to create an output prefix
FromDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.FromDescriptiveName
FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider
FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider
FromDimensionsBase<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
FromDualVoxelizedMarks - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
FromDualVoxelizedMarks() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromDualVoxelizedMarks
FromEntries - Class in org.anchoranalysis.plugin.io.bean.channel.map
FromEntries() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
fromFloat(VoxelBuffer<FloatBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
fromFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
fromFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg
FromFloat - Class in org.anchoranalysis.image.voxel.factory.sliceindex
FromHistogram - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Each input-file describes a histogram that produces one row of features.
FromHistogram() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
FromImage - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: An image that produces one row of features.
FromImage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
FromInput - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Finds the input-stack using a conventional name of input_image - and extracts the first channel
FromInput - Class in org.anchoranalysis.plugin.image.bean.stack.provider: Finds the input-stack using a conventional name of input_image
FromInput() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
FromInput() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
FromInt - Class in org.anchoranalysis.image.voxel.factory.sliceindex
fromIterable(Iterable<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list of features from an iterable
FromList - Class in org.anchoranalysis.bean.shared.color.scheme: Specifies a list of colors by a list.
FromList() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.FromList
FromMarkProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
FromMarkProposer() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
FromMarks - Class in org.anchoranalysis.plugin.mpp.bean.object.provider: Creates object-masks from a MarkCollection where (a particular region of) each mark creates an object.
FromMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
FromMask - Class in org.anchoranalysis.overlay.object.scaled
FromMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask
FromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask: Converts a binary-mask to an object-collection (containing a single object)
FromMask() - Constructor for class org.anchoranalysis.overlay.object.scaled.FromMask
FromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMask
FromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
FromMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: A base class for a ChannelProvider which also uses a binary-mask, but which doesn't use any other ChannelProvider as an input.
FromMaskBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
FromMetadata - Class in org.anchoranalysis.plugin.io.bean.channel.map
FromMetadata() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.FromMetadata
fromObject(ObjectMask) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
FromObjects - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert: Creates a Mask from a collection of object-masks
FromObjects - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
FromObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.source: Extracts features for each object in a collection.
FromObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
FromObjects() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
FromObjects() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
FromOutputName - Class in org.anchoranalysis.plugin.io.bean.descriptivename
FromOutputName() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
FromParamsBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
FromParamsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
fromPhysicalArea(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-area to pixels.
fromPhysicalArea(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-area to pixels.
fromPhysicalDistance(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-distance to voxels.
fromPhysicalDistance(double, DirectionVector) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-distance to voxels.
fromPhysicalVolume(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-volume to voxels.
fromPhysicalVolume(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts from physical-volume to voxels.
fromProvider(Provider<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list for a single-feature created from a provider
FromProvider - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
FromProvider() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
fromProviders(Collection<FeatureProvider<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list of features from a collection of feature-providers
fromRepeated(int, Supplier<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by repeatedly calling a function to create a single ObjectMask
FromSerializedMarks - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
FromSerializedMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
FromSerializedObject - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
FromSerializedObject() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
fromSet(Set<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection from a set of ObjectMask
fromShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
fromShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor: Creates a ImageProcessor from voxel-buffer (of type ShortBuffer) that is already a slice.
fromShort(SliceBufferIndex<UnsignedShortBuffer>, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor: Creates a ImageProcessor by extracting a slice from a SliceBufferIndex of type UnsignedShortBuffer.
fromShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
fromShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg
FromShort - Class in org.anchoranalysis.image.voxel.factory.sliceindex
FromSingle - Class in org.anchoranalysis.bean.shared.color.scheme: A single color repeated to meet the size.
FromSingle() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.FromSingle
FromSingleMark - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
FromSingleMark() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
fromSlice(Voxels<UnsignedByteBuffer>, int, String) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus: Creates an ImagePlus from one slice of a Voxels<UnsignedByteBuffer> voxels.
fromSlice(VoxelsWrapper, int) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
fromStack(Stack) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
FromStack - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Extracts a channel from a provider of a stack
FromStack() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
FromStack(ProviderAsStack) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
FromStackChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert
FromStackChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
FromStacks - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects a a subset of channels from a set of stacks
FromStacks() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.FromStacks
fromStream(Stream<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list of features from a stream
FromUnitValueDistance - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
FromUnitValueDistance() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
FromVoxelizedMarksWithEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
FromVoxelizedMarksWithEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromVoxelizedMarksWithEnergy
FromXmlList - Class in org.anchoranalysis.bean.define.adder: Adds a list of Named-Items define in a XML file in the current directory
FromXmlList() - Constructor for class org.anchoranalysis.bean.define.adder.FromXmlList
function(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DescriptionMatch
FunctionalIterate - Class in org.anchoranalysis.core.functional: Utilities for repeating operations a certain number of times.
FunctionalList - Class in org.anchoranalysis.core.functional: Utilities functions for manipulating or creating List in a functional way
FunctionalProgress - Class in org.anchoranalysis.core.functional: Utilities for updating a ProgressReporter in a functional way
functionAndType(String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DescriptionMatch

G

GaussianBlur2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
GaussianBlur2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
GaussianFromParams - Class in org.anchoranalysis.plugin.image.feature.bean.score
GaussianFromParams() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
GaussianSamplerFromParams - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
GaussianSamplerFromParams() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
GaussianScore<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.score
GaussianScore() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
GaussianScoreCalculator - Class in org.anchoranalysis.plugin.operator.feature.score: Calculates a Gaussian Score
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in interface org.anchoranalysis.mpp.feature.addcriteria.AddCriteria
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
generateIntersectingObjects(int, int, boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.IntersectingCircleObjectsFixture: Generates a number of circles that intersect and don't intersect
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.KernelIterDescriptionSerializerPeriodicReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
GenerateLabelHeadersForCSV - Class in org.anchoranalysis.plugin.image.task.feature: Generates a list of header-names for columns unrelated to features (identifiers and groups)
GenerateLabelHeadersForCSV(String[], Optional<String>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.GenerateLabelHeadersForCSV
generateNormal(double, double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a Gaussian (Normal) random variable with particular parameterization.
generateNormal(double, double) - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
generatePoisson(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a Poisson random variable with particular parameterization.
generatePoisson(double) - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.Mark
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.overlay.Overlay
GenerateToMatchObjects - Class in org.anchoranalysis.plugin.image.bean.color.provider: Generates colors to match the size of an object-collection
GenerateToMatchObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
GenerateUniqueParameterization - Interface in org.anchoranalysis.bean: Objects that must implement well-defined equals() and hashCode() methods and also generate a name uniquely identifying the class and all parameterization
Generator<T> - Interface in org.anchoranalysis.io.generator: A class that writes a particular type of object(s) to the filesystem.
GeneratorBridge<S,T> - Class in org.anchoranalysis.io.generator: Exposes a Generator<T> as if it was an Generator<S>.
Geometry - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
Geometry() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
Geometry(double, double) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
get() - Method in class org.anchoranalysis.core.cache.CachedSupplier
get() - Method in class org.anchoranalysis.core.concurrency.WithPriority
get() - Method in interface org.anchoranalysis.core.functional.checked.CheckedSupplier: Applies a supplier like with Supplier.get().
get() - Method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier: Gets the object being supplied to the store
get() - Static method in class org.anchoranalysis.core.progress.ProgressReporterNull
get() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput: Returns the underlying feature-input (independent of the session)
get() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
get() - Method in interface org.anchoranalysis.feature.session.strategy.child.CacheSupplier
get() - Method in class org.anchoranalysis.io.manifest.finder.FinderFileAsText
get() - Method in class org.anchoranalysis.io.manifest.finder.FinderKeyValueParams
get() - Method in class org.anchoranalysis.io.manifest.finder.FinderSerializedObject
get() - Method in interface org.anchoranalysis.io.manifest.finder.SerializedObjectSupplier
get() - Method in interface org.anchoranalysis.io.output.writer.ElementSupplier: Gets/creates the element to be written.
get() - Method in interface org.anchoranalysis.io.output.writer.ElementWriterSupplier: Gets/creates the ElementWriter to be used for an output.
get() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
get() - Method in class org.anchoranalysis.plugin.io.manifest.DeserializedManifest
get() - Method in interface org.anchoranalysis.plugin.operator.feature.score.FeatureResultSupplier
get(int) - Method in interface org.anchoranalysis.core.color.ColorIndex
get(int) - Method in class org.anchoranalysis.core.color.ColorIndexModulo
get(int) - Method in class org.anchoranalysis.core.color.ColorList
get(int) - Method in class org.anchoranalysis.core.color.SingleColor
get(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
get(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
get(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
get(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
get(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
get(int) - Method in interface org.anchoranalysis.core.index.GetterFromIndex
get(int) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
get(int) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
get(int) - Method in class org.anchoranalysis.feature.name.FeatureNameList
get(int) - Method in class org.anchoranalysis.feature.results.ResultsVector
get(int) - Method in class org.anchoranalysis.feature.results.ResultsVectorList
get(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
get(int) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
get(int) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
get(int) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
get(int) - Method in class org.anchoranalysis.image.core.stack.TimeSequence
get(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
get(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
get(int) - Method in interface org.anchoranalysis.io.bioformats.DestinationChannelForIndex
get(int) - Method in class org.anchoranalysis.io.manifest.directory.sequenced.DeriveElementsFromSequencedDirectory
get(int) - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection: An individual item in the collection.
get(int) - Method in class org.anchoranalysis.math.moment.ImageMoments
get(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
get(int) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
get(int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
get(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
get(int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
get(int) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
get(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
get(int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
get(int) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
get(int) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
get(int) - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
get(int) - Method in class org.anchoranalysis.spatial.box.BoundedList: Gets a particular element
get(int, int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
get(Class<? extends T>) - Method in class org.anchoranalysis.bean.BeanInstanceMap
get(String) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
get(String) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
get(String) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap: Returns null if non-existent
get(String) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
get(String) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
get(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
get(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.IndexedCSVRows
get(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.MapGroupToRow
get(Optional<String>) - Method in class org.anchoranalysis.io.output.outputter.InputOutputContextSubdirectoryCache: Gets (from the cache if it's already there) a context for a subdirectory of given-name
get(K) - Method in class org.anchoranalysis.core.cache.LRUCache
get(ProgressReporter) - Method in class org.anchoranalysis.core.progress.CachedProgressingSupplier
get(ProgressReporter) - Method in interface org.anchoranalysis.core.progress.CheckedProgressingSupplier
get(ProgressReporter) - Method in interface org.anchoranalysis.image.core.stack.NamedStacksSupplier
get(VoxelDataType) - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataTypeFactoryMultiplexer: Multiplexes one of the factories according to data-type
get(T) - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
get(T, int) - Method in interface org.anchoranalysis.plot.GetForSeries
getAboveMaxValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Constant to return if outside the range (above the maximum allowed)
getAcceptAll() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
getAdd() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
getAddCriteria() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
getAdditionalBackgrounds() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Additional background-stacks that are possible to use while annotating.
getAdditionalChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick: Additional channels other than the main one, which are located in the main raster file
getAdditionalChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: Additional channels other than the main one, which are located in the main raster file
getAdditionalPropertyPaths() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath: Additional property paths that are also changed, along with the main propertyPath *
getAddSum() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum: Added to all gradients (so we can store negative gradients)
getAdjacentChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: Channels that are located in a separate raster file adjacent to the main raster file
getAfterPreoperation() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject: After pre-operation but before scaling
getAggInterval() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
getAggIntervalLog10() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval: How many iterations before printing a new report? Encoded in log10.
getAggregateReceiver() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
getAggregateTriggerBank() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
getAll() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component
getAllCacheNames() - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
getAllKernelFactories() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
getAllowsChildren() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
getAngle() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle: Angle part of axis-angle orientation (in radians)
getAngleDegrees() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
getAngleDegrees() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
getAngleRadians() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
getAnnealScheme() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
getAnnotations() - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
getAnnotatorStrategy() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
getAppendChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: Channels that are located in a separate raster file somewhere else in the project's structure
getAppendCsv() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
getAppendCSV() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
getAppendHistogram() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
getAppendObjects() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: Appends object-collections to the multi-input
getAppendStack() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
getArbitrary() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
getArbitraryElement() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider: Gets one element of the provider (arbitrarily)
getArrange() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
getArrange() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
getAsBoolean() - Method in interface org.anchoranalysis.core.functional.checked.CheckedBooleanSupplier: Applies a supplier like with BooleanSupplier.getAsBoolean().
getAssigner() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
getAssignMode() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
getAssociatedElementRange() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
getAssociatedElementRange() - Method in interface org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectory: The associated element-range with ths folder.
getAssociatedMark() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
getAsSupplier(String) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
getAxis() - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector: Which axis the unit-vector will align with.
getAxis() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle: Axis part of axis-angle orientation (should be normalized)
getAxis() - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
getAxis() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis: Which axis? X=0, Y=1, Z=2
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation: Which axis to read from (x,y,z)
getAxis() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
getAxisColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
getAxisMax() - Method in class org.anchoranalysis.plot.AxisLimits
getAxisMin() - Method in class org.anchoranalysis.plot.AxisLimits
getBackground() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
getBackground() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack: The background
getBackground() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The background.
getBackgroundChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Uses only this channel (identified by an index in the stack) as the background, -1 disables.
getBackgroundChannelName() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
getBackgroundChannelProvider() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
getBackgroundColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
getBackgroundID() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
getBackgroundStackMap() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-null, maps underlying stack-name to a background
getBackgroundStackName() - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
getBeanExtension() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
getBeanExtension() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
getBeanName() - Method in class org.anchoranalysis.bean.AnchorBean: A short-name identifying a bean (by default the name of the class associated with the bean).
getBelowMinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Constant to return if outside the range (below the minimum allowed)
getBest() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
getBest() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
getBestState() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
getBinaryInputChannelID() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform: The ID of the binary input mask that determines the region of the watershed
getBinarySgmn() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
getBirthRepeats() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
getBitsPerPixel() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
getBlockSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The block-size as per OpenCV implementation (identical default-size)
getBlockStride() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The block-stride as per OpenCV implementation (identical default-size)
getBlue() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
getBlue() - Method in class org.anchoranalysis.core.color.RGBColor
getBlue() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
getBorderWidth() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Adds a border around each part of the montage
getBoundCalculator() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
getBoundCalculator() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
getBoundRadius() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
getBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
getBoundsRatio() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
getBoundType() - Method in class org.anchoranalysis.core.index.bounded.BoundChangeEvent
getBridgeMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each input-object to an intermediary-object
getBundleSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
getBundleSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
getCache() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
getCache() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
getCache() - Method in class org.anchoranalysis.feature.session.strategy.replace.CacheAndReuseStrategy
getCacheNames() - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
getCacheSize() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches: Size of feature evaluation cache for featureEvaluatorMatch
getCalculateLevel() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
getCalculateLevel() - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: Method to calculate the level for a particular object.
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold: Calculates the level for the threshold
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
getCalculateLevelElse() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
getCalculator() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
getCellDefault() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
getCells() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
getCellSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The cell-size as per OpenCV implementation (identical default-size)
getCenter() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
getCenterPoint() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
getCenterPointX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
getCenterPointY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
getChangedMarkIDArr() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
getChangedMarkIDs() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
getChannel() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A channel that is provided to the stack.
getChannel() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
getChannel(int) - Method in class org.anchoranalysis.feature.energy.EnergyStack
getChannel(int) - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
getChannel(int) - Method in class org.anchoranalysis.image.core.stack.Stack
getChannel(int) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
getChannel(String) - Method in class org.anchoranalysis.plugin.image.task.channel.ChannelGetterForTimepoint
getChannel1() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
getChannel1() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
getChannel2() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
getChannel2() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
getChannel3() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
getChannelAssignFrom() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
getChannelChecker() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState
getChannelConversionStyle() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: To convert as RGB or independently or in another way
getChannelConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
getChannelConverter() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: Optionally, how to convert from one bit-depth to another (scaling, clipping etc.)
getChannelElse() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
getChannelFilter() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: Optionally, includes only certain channels when converting.
getChannelFirst() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of first channel
getChannelGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
getChannelID() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: The ID of the channel that provides the input to the filter
getChannelIfVoxelZero() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero: If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
getChannelIndex() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick: If either stackAsChannel==true or we have specified additionalChannels this indicated which channel to use from the stack
getChannelLookup() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
getChannelMap() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
getChannelMask() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: If defined, this is the name of channel used as a mask over the values which are fed into the histogram
getChannelName() - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
getChannelName() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack: By default all channels are converted into a stack.
getChannelNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
getChannelNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
getChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
getChannelSecond() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of second channel
getChannelsExtra() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getChannelsPerByteArray() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
getChannelThreshold() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
getChannelType() - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker
getChart() - Method in class org.anchoranalysis.plot.PlotInstance
getCheck() - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
getChecked() - Method in class org.anchoranalysis.io.output.outputter.Outputter: Gets the underlying delegate of Outputter that throws checked-exceptions instead of using a ErrorReporter.
getCheckMark() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
getCheckMark() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
getCheckMark() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
getCheckParsedFilePathBag() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles: Imposes a condition on each parsedFilePathBag which must be-fulfilled if a file is to be included
getChildAt(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
getChildCount() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
getClassifierProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
getClassLoader() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
getClassOfTarget() - Method in class org.anchoranalysis.bean.initializable.property.ExtractFromParam
getCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
getCol() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
getCol(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
getColForListIndex(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
getCollection() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
getCollectionID() - Method in class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
getCollectionID() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
getColor() - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle: The single color to repeat.
getColor() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: An optional color associated with the label when displayed via GUI
getColor() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
getColor(int) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
getColorIDGetter() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: Gets a color ID associated with the object
getColorIndex() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: Colors for a given index
getColorList() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
getColorList() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
getColors() - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary: The delegate that creates the (unshuffled) list.
getColors() - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList: The list of colors to specify
getColors() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator: Colors to use for drawing objects
getColors() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: The colors in the collection.
getColorScheme() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
getColorsUnpaired() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
getColorUnselectedObjects() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Optionally outline the other (unselected for the thumbnail) objects in this particular color.
getColumnDefinition() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV: Column definition for the CSVfiles
getColumnFirstNumberPixels() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with the number of pixels for the first Object
getColumnFirstPointX() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with X coordinate of point for the first Object
getColumnFirstPointY() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with Y coordinate of point for the first Object
getColumnFirstPointZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with Z coordinate of point for the first Object
getColumnGroup() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition: Name of CSV column used to group results (the same values, are outputted together)
getColumnID() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition: Name of CSV column with the file identifier
getColumnNumPixels() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single: Name of CSV column with the number of pixels for the first Object
getColumnPointX() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single: Name of CSV column with X coordinate of point for the first Object
getColumnPointY() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single: Name of CSV column with Y coordinate of point for the first Object
getColumnPointZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single: Name of CSV column with Z coordinate of point for the first Object
getColumns() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: How many columns to use in the montage, or 0 to guess an approximately square output
getColumnSecondNumberPixels() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with the number of pixels for the second Object
getColumnSecondPointX() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with X coordinate of point for the first Object
getColumnSecondPointY() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with Y coordinate of point for the first Object
getColumnSecondPointZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with Z coordinate of point for the first Object
getCombine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
getCombined() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix: A path that combines the directory and fileNamePrefix.
getCombined() - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
getCombined() - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
getCommand() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation: One of: open, close, fill, erode, dilate, skel, outline
getCommandName() - Method in class org.anchoranalysis.launcher.config.HelpConfig: What the application command is described as in the help message e.g. anchor or anchorGUI
getComparerLeft() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
getComparerMultiplex(boolean) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
getComparerRight() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
getComparers() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
getCondition() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
getCondition() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
getConfidence() - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
getConfidenceThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects: The maximum difference in confidence for merging.
getConfigDir() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: the directory where configuration files are stored
getConnPoint() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
getConstant() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
getConstantBound() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
getContains() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
getContains() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must contain (case-sensitive) this string.
getContext() - Method in class org.anchoranalysis.core.identifier.provider.store.SharedObjects: Logger and other common configuration
getContext() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
getContext() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
getConvert() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
getConverters() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
getCopyFilesMethod() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
getCopyFilesNaming() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
getCopyFilesNaming() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
getCost() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeStrategy
getCost(int, int) - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: Gets the cost from an element from the first-list to an element from the second-list.
getCosts() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentObjectFactory
getCount() - Method in class org.anchoranalysis.math.arithmetic.Counter
getCount() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: The running count
getCount() - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
getCount(int) - Method in class org.anchoranalysis.math.histogram.Histogram
getCountThreshold() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: If there are more than countThreshold elements, use summarizerGreaterThan, else summarizerElse.
getCountXY() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint: The count for XY dimensions (guaranteed to always be the same
getCountZ() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint: The count for Z dimension (this is identical to RunningSumPoint.getCountXY() if only 3D points have ben added)
getCreateMark() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
getCsvFeaturesAggregated() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames: The CSV of aggregated feature-results, if enabled.
getCsvFeaturesGroup() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames: The CSV individually written for each group, if enabled.
getCsvFeaturesNonAggregated() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames: The CSV of non-aggregated feature-results
getCsvFilePath() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
getCsvFilePath() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
getCurrent() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
getCurrent() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
getCurrentTemp() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
getCustomName() - Method in class org.anchoranalysis.feature.bean.Feature: An optional additional name that be associated with the feature (defaults to an empty string)
getDatasetName() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: The name of the experiment including version suffix
getDatasets() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
getDatasets() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
getDatasetSpecific() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
getDatasetSpecific() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
getDatasetSuffix() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase: A suffix appended to the dataset name extracted from the reg exp
getDatasetVersion() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: A version-suffix appended to the dataset name extracted from the reg exp
getDefault() - Static method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues: Default values to use, if not otherwise specified
getDefault() - Static method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
getDefaultBeanClass() - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory: Returns null as Optional is not supported by BeanFactory interface.
getDefaultColors() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: The default color-scheme used for outputs, if no other scheme is specified.
getDefaultInstances() - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
getDefaultInstances() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
getDefine() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
getDefine() - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop: Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
getDefine() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Adds definitions of stacks/objects etc.
getDelaySizeAtEnd() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
getDelegate() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
getDelimiter() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
getDelta() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getDeltat() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
getDepth() - Method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
getDerivePath() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
getDerivePath() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
getDescription() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
getDescription() - Method in class org.anchoranalysis.io.manifest.ManifestDirectoryDescription
getDescription() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
getDescription() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
getDestination() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
getDestination() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
getDestination() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.DualVoxelizedMarks
getDestination() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
getDestinationFolderPath() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
getDimensions() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Dimensions to create new mask
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
getDimensions() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getDimensions() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
getDimensions() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
getDimensionsOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
getDimensionsRequired() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
getDimensionsSource() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
getDimensionsTarget() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
getDirection() - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance: Direction of the distance being converted, defaults to a unit vector along the X-axis
getDirection() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
getDirectionVector() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
getDirectionVector() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
getDirectory() - Method in class org.anchoranalysis.core.system.path.PathDifference: The directory component of the difference, if it exists.
getDirectory() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget: The directory to which the output-manager is bound to.
getDirectory() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
getDirectory() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory: A relative-path (to the user home directory) which is used as an output directory
getDirectoryDistance() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment: How many directories to recurse back from the current file to the Experiments/ directory
getDistance() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
getDistance() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors: How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
getDistance() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
getDistanceMapProvider() - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters: A distance map which can also be used for making decisions on merging
getDistanceMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
getDistanceTransformMultiplyBy() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform: Multiplies the distance transform by this factor to make it more meaningful in a short
getDistanceTransformSmoothSigmaMeters() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform: If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below
getDistanceX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
getDistanceY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
getDistanceZ() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
getDistanceZEndIfEmpty() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
getDivideByZeroValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
getDivisor() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble: Divide by
getDivisor() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo: What the identifier is divided by to find the modulo.
getDoubleOrNull(int) - Method in class org.anchoranalysis.feature.results.ResultsVector
getDrawObject() - Method in class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
getDrawObject() - Method in class org.anchoranalysis.overlay.writer.DrawOverlay
getDscr() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
getDscr() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
getDualStack() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
getEigenvalue() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
getEigenvector() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
getElemAllAsFeatureList() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
getElemAllCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
getElemByCliqueSize(int) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
getElement() - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
getElemIndAsFeatureList() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
getElemIndCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
getElemPairAsFeatureList() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
getElemPairCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
getEllipseSum(double, double, DoubleMatrix2D) - Static method in class org.anchoranalysis.mpp.mark.conic.Ellipse
getEllipsoidCalculator() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
getEllipsoidSum(double, double, double, DoubleMatrix2D) - Static method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
getEmptyValue() - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
getEnd() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: An index beyond which we cannot iterate (inclusive)
getEndPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
getEnergy() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
getEnergyChannelIndexCheck() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
getEnergyChannelIndexFail() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels: Index of which channel in the energy-stack to select
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase: Index of which channel in the energy-stack to select
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel: Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: The channel that that forms the histogram
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask: The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
getEnergyIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
getEnergyIndexGradient() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
getEnergyIndexMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: A channel of the energyStack that is used as an additional mask using default byte values for ON and OFF
getEnergyIndexMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Optionally, index of another channel that masks the histogram.
getEnergyIndexX() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
getEnergyIndexY() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
getEnergyIndexZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
getEnergyParamsName() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop: If non-empty, A keyValueParams is treated as part of the energyStack
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Associated Energy Scheme, which should include the EnergySavedPairs
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
getEnergyScheme() - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
getEnergyScheme() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
getEnergySchemeCreator() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
getEnergySchemeCreator() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Creates an energy scheme that assigns an energy score to each collection of marks.
getEnergyStack() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
getEnergyStack() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
getEnergyStack() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack: The energy-stack
getEnergyStack() - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider
getEnergyStack() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
getEnergyStackOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: Returns the energy-stack which may or not be present
getEnergyStackRequired() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: Returns the energy-stack or throws an exception if it's not set as it's required.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The pre-annealed total energy
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Pairwise energy total
getEquals() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must be exactly equal to (case-sensitive) this string.
getErrorMessage() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
getErrorNode() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
getErrorReporter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: The associated error reporter.
getErrorReporter() - Method in class org.anchoranalysis.io.output.outputter.Outputter
getErrorReporter() - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
getErrorTree() - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
getExactDepth() - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
getException() - Method in exception org.anchoranalysis.core.functional.CheckedStream.ConvertedToRuntimeException
getException(int) - Method in class org.anchoranalysis.feature.results.ResultsVector
getException(String) - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider: Retrieves the item if it exists, or throws an exception if it doesn't exist.
getException(String) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
getException(String) - Method in class org.anchoranalysis.feature.shared.SharedFeatureSet
getExecutionTime() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
getExecutionTime() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
getExperimentalManifest() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
getExperimentArguments() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
getExperimentArguments() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
getExperimentDescription() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
getExperimentIdentifier() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: A name for the experiment.
getExperimentIdentifier() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
getExperimentIdentifier() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
getExperimentManifest() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase: A folder identifying the type of experiment (where the outputs are all put in the same directory
getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: A folder identifying the type of experiment (where the outputs are all put in the same directory
getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment: The value of $1 (see comment above) in naming-structure.
getExpression() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
getExtension() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
getExtension() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
getExtensionHTML() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
getExtensionSerialized() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
getExtensionText() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
getExtensionXML() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
getExtra() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
getExtractScoreSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
getExtractScoreSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
getExtractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
getExtractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
getExtractWeight() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
getFactor() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
getFactor() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
getFactorHigh() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
getFactorLow() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
getFactorStdDev() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
getFallback() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
getFallbackName() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If there's no task-name, then this constant is used as a fallback name
getFeature() - Method in class org.anchoranalysis.feature.bean.list.ListSequence: The list feature that is duplicated, and populated.
getFeature() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
getFeature() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session
getFeature() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getFeature() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Feature that calculates the score for an object.
getFeature() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
getFeature() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
getFeature() - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
getFeature() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
getFeatureCondition() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
getFeatureCondition() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange: Calculates value for the condition - which is checked if it lies within a certain range
getFeatureElse() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
getFeatureEvaluator() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
getFeatureEvaluator() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
getFeatureEvaluatorMatch() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
getFeatureEvaluatorMerge() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
getFeatureEvaluatorThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Allows merge only if the feature-value satisfies a relation to this threshold
getFeatureListRef() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
getFeatureListSet() - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
getFeatureNameIndex() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
getFeatureNames() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
getFeatureNames() - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
getFeatures() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator: A list of providers, combined together to form a list of features, to be calculated in a session
getFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: The features to be exported (after possibly some manipulation or augmentation)
getFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: Features to calculate for objects in the features output.
getFeaturesAggregate() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Features applied to each group to aggregate values (takes FeatureResultsVectorCollection)
getFeaturesImage() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Additional features that only depend on the image, so do not need to be replicated for every object.
getFeaturesPair() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Additional features that are processed on the pair of images (i.e.
getFeatureTables() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop: Specifies a feature-table that can also be outputted.
getFeedbackReceiver() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
getFeedbackReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Processes feedback from the segmentation algorithm for outputting / debugging.
getFileExtension() - Method in class org.anchoranalysis.io.manifest.file.FileType
getFileFilter() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: Files to search for
getFileId() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv: Unique identifier for the stack, object-mask-collection etc.
getFileId() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManagerWithFileID: Unique identifier for the stack, object-mask-collection etc.
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
getFileInput() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment: A string indicating the input file(s)
getFilename() - Method in class org.anchoranalysis.core.system.path.PathDifference: The file-name component of the difference, if it exists.
getFileName() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
getFileName() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
getFilenamePrefix() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
getFilenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
getFilenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: The filename to be written, including prefix, suffix, etc.
getFilenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
getFilenameWithoutExtension(int) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Like IndexableOutputNameStyle.getFilenameWithoutExtension() but incorporates an integer index.
getFilenameWithoutExtension(String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Like IndexableOutputNameStyle.getFilenameWithoutExtension() but incorporates an string index.
getFilePath() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getFilePath() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
getFilePath() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
getFilePath() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
getFilePathParser() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
getFilePathParser() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
getFilePathPrefixer() - Method in class org.anchoranalysis.io.output.bean.OutputManager: Determines a prefix to use when outputting a file based upon an input-path.
getFilePathPrefixer() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
getFilePathPrefixer() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
getFilePathProviderSVM() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
getFilePrefix() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
getFiles() - Method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
getFilesProvider() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
getFilesProvider() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles: The files to use as inputs.
getFilesProvider() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
getFilesProvider() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: A path to the main channel of each file
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
getFilter() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
getFilterFilesCsv() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: If set, a CSV is read with two columns: the names of images and a
getFilterInitParams(Path) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
getFindOutlinePixelAngle() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
getFirst() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
getFirst() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
getFirst() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the first-level.
getFirst() - Method in class org.anchoranalysis.mpp.segment.transformer.Compose: First transformation from S to U
getFirst() - Method in class org.anchoranalysis.overlay.writer.PrecalculationOverlay
getFirst() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
getFirstArgument() - Method in class org.anchoranalysis.launcher.config.HelpConfig: What the application argument is described as in the help message e.g. experimentFile.xml
getFirstBinaryValues() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
getFirstBinaryValuesByte() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
getFirstDimensions() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
getFirstExtent() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
getFirstPoint() - Method in class org.anchoranalysis.spatial.Contour
getFlatBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
getFloat() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
getFolderDataset() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
getFolderOutput() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
getFolderPath() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
getForAllSlices(int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
getForceReader() - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader: If non-empty forces usage of a particular bioformats plugin
GetForSeries<T,S> - Interface in org.anchoranalysis.plot
getForSlice(int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
getForward() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
getFoundDirectory() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
getFoundFile() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
getFoundOrLog(String, Logger) - Method in interface org.anchoranalysis.annotation.io.image.findable.Findable: Returns the found object (or empty() if it's not found.....
getFoundOrLog(String, Logger) - Method in class org.anchoranalysis.annotation.io.image.findable.Found
getFoundOrLog(String, Logger) - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
getFriendlyName() - Method in class org.anchoranalysis.feature.bean.Feature
getFriendlyName() - Method in interface org.anchoranalysis.feature.calculate.InitializableFeature: A friendly name that can be displayed to user describing the Feature.
getFrom() - Method in class org.anchoranalysis.core.graph.TypedEdge: The vertex the edge joins from.
getFuncScore() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.AccptProbCalculator
getFunction() - Method in class org.anchoranalysis.io.manifest.ManifestDescription: Identifies the function the entity plays.
getGaussianSigmaMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
getGenerator() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter: The generator to be (repeatedly) used to write elements in the sequence.
getGradient() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getGraphColorScheme() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
getGrayscaleReconstruction() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
getGreen() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
getGreen() - Method in class org.anchoranalysis.core.color.RGBColor
getGreen() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
getGroup() - Method in class org.anchoranalysis.feature.io.csv.RowLabels: an identifier for a higher-level group which the row belongs to (foreign key)
getGroup() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Specifies a group for the label (similar labels that are displayed together)
getGroup() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: If non-null this file-path is used to determine the group of the file If null, no group is included.
getGroup() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: If defined, translates a file-path into a group.
getGroup() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
getGroup() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
getGroupGeneratorName() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
getGroupHeaders() - Method in class org.anchoranalysis.feature.io.results.LabelHeaders: Headers describing the non-feature columns outputted in the CSV related to identifying the group of a row
getGroupMap() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState
getGroupNum() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
getHeaders() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata: Headers for the CSV file
getHeight() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
getHistogram() - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
getHistogram() - Method in class org.anchoranalysis.image.feature.histogram.FeatureInputHistogram
getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram: If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional histogram of voxel intensity values which can be used by segment
getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram: The histogram to plot.
getHistogram() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
getHistogram() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram: If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
getHistogramChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
getHistogramIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
getHistogramsExtra() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getHistogramsOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.

What's allowed or not when outputting histograms
getHorizontalAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
getId() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
getId() - Method in class org.anchoranalysis.feature.bean.operator.Reference
getId() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
getId() - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
getId() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
getId() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
getId() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
getId() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
getId() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
getId() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
getId() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference
getId() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
getId() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
getId() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: ID for the particular object-collection
getId() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Translates an input file name to a unique ID
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
getId() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
getId() - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
getIdentifier() - Method in class org.anchoranalysis.mpp.mark.Mark
getIdentifier() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
getIdentifier() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
getIdentifier() - Method in interface org.anchoranalysis.overlay.identifier.Identifiable
getIdentifier() - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
getIdentifier(ObjectWithProperties, int) - Method in class org.anchoranalysis.image.core.object.properties.IdentifierByProperty
getIdentifier(ObjectWithProperties, int) - Method in class org.anchoranalysis.overlay.identifier.IdentifyDelegateToOverlays
getIdentifier(Mark, int) - Method in class org.anchoranalysis.mpp.mark.IdentifierFromMark
getIdentifier(Overlay, int) - Method in class org.anchoranalysis.overlay.identifier.IdentifierFromOverlay
getIdentifier(T, int) - Method in interface org.anchoranalysis.core.identifier.getter.IdentifierGetter
getIdentifier(T, int) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
getIdentifier(T, int) - Method in class org.anchoranalysis.core.identifier.getter.IdentifyByIteration
getIdentifierSuffix() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
getIdentifierSuffix() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
getIdGenerator() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
getIdGetter() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
getIdGetter() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: Gets a unique ID associated with the object
getIfPresent(K) - Method in class org.anchoranalysis.core.cache.LRUCache: Gets an value if present, but doesn't create any new entry if it's absent.
getIgnoreContains() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-empty any stackNames (after map) containing a certain string will be ignored
getImage() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
getImage() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getImage() - Method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
getImageDimensions() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
getImageInit() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
getImageLabeller() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: Maps a label to an image
getImgChannelMapCreator() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
getIncrement() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: Size of step to use when incrementing
getIncrementDegrees() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
getIncrementDegrees() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
getIndex() - Method in class org.anchoranalysis.core.index.Indexable
getIndex() - Method in interface org.anchoranalysis.core.index.IndexGetter
getIndex() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
getIndex() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
getIndex() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
getIndex() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
getIndex() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt: Index in z-dimension of slice to extract
getIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase: Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
getIndex() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
getIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
getIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
getIndex() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: Which index to return from the HOG descriptor
getIndex(String) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
getIndex(TreeNode) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
getIndexedRowsOrCreate(Path, ColumnDefinition) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVSharedState
getIndexForMemo(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
getIndexNonZero() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
getIndividual() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
getInitContext() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
getInitializationParameters() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
getInitialKernel() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
getInitialPoint() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
getInitParams() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
getInitParamType() - Method in class org.anchoranalysis.bean.initializable.property.PropertyInitializer
getInnerCoreDistance() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
getInPathPrefix() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
getInput() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
getInput() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: The input-manager to specify where/which/how necessary inputs for the experiment occur.
getInput() - Method in class org.anchoranalysis.experiment.task.InputBound
getInput() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
getInput() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
getInput() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
getInput() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
getInput() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.Shuffle
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
getInput() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
getInputDebug() - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
getInputDirectory() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments: A directory indicating where inputs can be located
getInputFilterExtensions() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments: If defined, a set of extension filters that can be applied on inputDirectory
getInputIfPresent(T) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
getInputName() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
getInputName() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
getInputName() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
getInputOutputContext() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
getInputPaths() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
getInputPointShift() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
getInstance() - Static method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
getInt(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Gets an element from the buffer at a particular position, converting, if necessary, to an int.
getInt(int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
getInt(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
getIntensity() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getIntensityHistogram() - Method in class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Interpolator used when scaling the background
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
getItem() - Method in class org.anchoranalysis.bean.NamedBean: The item that is to be named (i.e.
getItem() - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
getItem() - Method in class org.anchoranalysis.feature.bean.list.DefineSingle
getItem() - Method in class org.anchoranalysis.feature.bean.list.PrependName
getItem() - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
getItem() - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
getItem() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: For each feature in the list, a corresponding "aggregate" feature is created in the output list
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Feature to apply to the histogram
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Feature to apply to the histogram
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
getItem() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity: Feature to apply to the histogram
getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoOne
getItem1() - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
getItem2() - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
getItemMean() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
getItemProportionate() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
getItemStdDev() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
getIteration() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
getIterations() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat: The maximum number of iterations.
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection: The number of dilations and erosions to apply to determine if two objects intersect
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: The number of dilations and erosions to apply and whether to do in the Z dimension
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell: The number of dilations and erosions to apply and whether to do in the Z dimension
getIterations() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation: iterations for erode, dilate, open, close
getIterations() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
getIterationsDilation() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological dilation
getIterationsErosion() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological erosion
getJobDescription() - Method in class org.anchoranalysis.experiment.task.processor.SubmittedJob
getJobManifest() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
getJobNumber() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
getJobShortName() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
getJobState() - Method in class org.anchoranalysis.experiment.task.processor.SubmittedJob
getKappa() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
getKeep() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
getKeepProcessorsFree() - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor: How many processors to avoid using for the tasks.
getKeepProcessorsFree() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: How many processors to avoid using for the tasks.
getKernel() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
getKernel() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
getKernel() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
getKernel() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
getKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
getKernelAccepted() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
getKernelCalcContext() - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
getKernelFactoryList() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
getKernelHalfWidth() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median: Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
getKernelNegative() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
getKernelNoProposalDescription() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
getKernelPositive() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
getKernelProposed() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
getKernelProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Proposes kernel-changes during iterations of hte marked-point-processes.
getKernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
getKey() - Method in exception org.anchoranalysis.core.index.GetOperationFailedException
getKey() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
getKey() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getKey() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
getKey() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
getKey() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
getKey() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
getKey() - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
getKeyGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
getKeyLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
getKeyMean() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
getKeyPrefix() - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param: Prefix prepended to key
getKeyStdDev() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
getKeySuffix() - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
getKeyUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
getKeyValueParams() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
getKeyValueParamsID() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
getKeyValueParamsID() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage: If non-empty, the identifier of a key-value-params collection that is passed to the segmentation procedure.
getLabel() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation: The label that applies to the image
getLabelMap() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
getLabels() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
getLabels() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
getLast() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
getLastDivider() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
getLastPoint() - Method in class org.anchoranalysis.spatial.Contour
getLastPoints1() - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
getLastPoints2() - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
getLeafDirectories() - Method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
getLeft() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare: Objects on left-side of the comparison
getLevel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
getLevel() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
getLine() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
getList() - Method in class org.anchoranalysis.bean.define.adder.Concatenate
getList() - Method in class org.anchoranalysis.bean.shared.regex.RegExList
getList() - Method in class org.anchoranalysis.bean.shared.StringMap
getList() - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple: The list of loggers to log to
getList() - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
getList() - Method in class org.anchoranalysis.feature.bean.list.Define
getList() - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed
getList() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
getList() - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
getList() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
getList() - Method in class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
getList() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
getList() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
getList() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
getList() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
getList() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
getList() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
getList() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine: A list of other filters from which the sub-classes implement filtering behaviour.
getList() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
getList() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence: A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
getList() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
getList() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
getList() - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
getList() - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate
getList() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Combine
getList() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
getList() - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
getList() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
getList() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
getList() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
getList(Class<?>) - Method in class org.anchoranalysis.bean.define.Define
getListAdditionalChannelProviders() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
getListAppend() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
getListAppend() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick: Additional entities that are appended to the multi-input
getListAppendFilePath() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
getListAppendKeyValueParams() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
getListAppendMarks() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
getListAppendMarksFromAnnotation() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
getListAppendMarksFromAnnotationAcceptedOnly() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
getListAppendMarksFromAnnotationRejectedOnly() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
getListComparers() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
getListFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendFilePath
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendMarks
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendObjects
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManager
getListImageFeatures() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
getListImageFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
getListPaired(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
getListPaired(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
getListPaired(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
getListReportFeatures() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
getListReportFeatures() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
getListStackProvider() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages: The channels we extract the object-masks from - all assumed to be of same dimension
getListStackProviderMIP() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages: The channels we extract the object-masks from - all assumed to be of same dimension
getListUnassigned(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
getListUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
getListUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
getListUnassignedLeft() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
getListUnassignedRight() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
getLocal(int) - Method in class org.anchoranalysis.image.voxel.kernel.LocalSlices
getLocalPath() - Method in class org.anchoranalysis.bean.AnchorBean: A local path on the filesystem associated with this bean (from serialization) if defined.
getLog() - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf: The logger to use if conditions are fulfilled
getLog() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
getLogExperiment() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Where log messages that do not pertain to a specific job (input) appear.
getLogExperimentPath() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment: Relative path to a logger for the experiment in gneeral
getLogger() - Method in class org.anchoranalysis.bean.initializable.InitializableBean: The logger
getLogger() - Method in class org.anchoranalysis.core.log.CommonContext: The logger
getLogger() - Method in class org.anchoranalysis.experiment.task.InputBound
getLogger() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
getLogger() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: The associated logger.
getLogger() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
getLogger() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
getLogger() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
getLogger() - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
getLogger() - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
getLogger() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
getLoggerExperiment() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
getLoggerTaskCreator() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
getLogReporterJob() - Method in class org.anchoranalysis.experiment.task.InputBound
getLogTask() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: Where log messages that do pertain to a specific job (input) appear.
getLogTaskPath() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment: Relative path to a logger for a specific task
getLookup() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
getMainChannelIndex() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: Index of the mainChannel
getMainChannelName() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: The name of the channel provided by the rasters in file Provider
getMainObjectName() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
getMainObjectName() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
getMajorAxisAngle() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
getMajorAxisSlope() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
getManifest() - Method in class org.anchoranalysis.experiment.task.InputBound
getManifestDescription() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern: A manifest-description for the directory, if defined.
getManifestDescription() - Method in class org.anchoranalysis.io.manifest.file.FileType
getManifestDescriptionFunction() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
getManifestDeserializer() - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
getManifestExperimentInputFileSet() - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
getManifestFunction() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
getManifestFunction() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
getManifestInputFileSet() - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
getMap() - Method in class org.anchoranalysis.mpp.io.input.OperationMap
getMap() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
getMap() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
getMark() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
getMark() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: The associated mark
getMark() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
getMark() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
getMark() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
getMarkBounds() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams: Backwards compatible for when we only had a single bounds
getMarkBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
getMarkBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
getMarkBoundsSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getMarkEvaluator() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: A mark-evaluator that is added to the GUI to support this annotation
getMarkFactory() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
getMarkFactory() - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
getMarkFactory() - Method in class org.anchoranalysis.mpp.segment.kernel.MarkFactoryContext
getMarkFactory() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
getMarkFactory() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Creates a new mark, before perhaps further manipulations by a kernel.
getMarkFactory() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
getMarkFromMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
getMarkMergeProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getMarkProposer() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Name of the MarkProposer to use.
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
getMarkProposerAdditionalBirth() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
getMarkProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getMarkProvider() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
getMarkProvider() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
getMarkProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
getMarkProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
getMarkProvider() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
getMarkRmv() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
getMarks() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
getMarks() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The marks
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
getMarks() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
getMarks() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
getMarks() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
getMarks() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
getMarks() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition
getMarksAfter() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
getMarksAfterOptional() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
getMarksCollection() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getMarksColored() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
getMarksOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.

What's allowed or not when outputting configurations
getMarkSplitProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
getMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
getMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
getMarksProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getMarksReject() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Marks covering area that should be rejected, can be null
getMarksWithTotalEnergy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
getMask() - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getMask() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
getMask() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional mask which restricts the algorithm to only parts of the channel where the mask has an ON voxel
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
getMask() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
getMask() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A mask that is provided to the stack.
getMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
getMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
getMask() - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
getMask() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
getMask() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
getMask() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
getMaskElse() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase: Returned instead of mask if the predicate is not satisfied
getMaskFilled() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
getMaskFilled() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
getMaskIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
getMaskOutline() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
getMaskValue() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: What voxel value to read as "On" in the mask above.
getMaskValue() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
getMatch() - Method in class org.anchoranalysis.feature.bean.list.SelectFromShared
getMatch() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
getMatch() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
getMatches() - Method in class org.anchoranalysis.image.core.object.MatchedObject: The matches associated with the source-object
getMatchString() - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
getMatrix() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: A two-dimensional array mapping the costs from first to second
getMatrix() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
getMavenProperties() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
getMax() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
getMax() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
getMax() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
getMax() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
getMax() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
getMax() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
getMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Maximum-boundary for acceptable range
getMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
getMax() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature: Calculates maximally-allowed range boundary
getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars: Boundary value indicating maximally-allowed range value
getMaxBin() - Method in class org.anchoranalysis.math.histogram.Histogram: Maximum bin-value inclusive
getMaxCost() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
getMaxCost() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
getMaxDirectoryDepth() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
getMaxDistance() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: An optional maximum distance
getMaxDistance() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
getMaxDistance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
getMaxDistanceBetweenMinima() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
getMaxDistanceCOG() - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters: The maximum distance allowed between center-of-gravities of objects
getMaxDistanceDeltaContour() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform: The maximum distance allowed between two seeds in terms of their values in the distance map
getMaxDistanceDeltaContour() - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters: The maximum distance allowed between the 'distance from contour' values provided from the distanceMap for each point.
getMaxDistanceProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
getMaxDistanceZ() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
getMaximumIndex() - Method in interface org.anchoranalysis.core.index.bounded.BoundedRange
getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
getMaxNumber() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
getMaxNumberItems() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Limit
getMaxNumberProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor: An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
getMaxNumberProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: Theoretical maximum number of (CPU) processors to use in parallel.
getMaxNumberProcessors() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment: An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
getMaxNumberProcessors() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
getMaxNumItems() - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
getMaxNumItems() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
getMaxOfMax() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
getMaxSize() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMaxSplitGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
getMaxValue() - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker
getMaxVar() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMaxVolume() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
getMaxX() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Maximum X coordinate inclusive
getMaxY() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Maximum Y coordinate inclusive
getMaxZ() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Maximum Z coordinate inclusive
getMean() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic: Mean
getMean(int) - Method in class org.anchoranalysis.math.moment.ImageMoments: Index is the axis (0 for X, 1 for Y, 2 for Z)
getMedianRadiusMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
getMemoForIndex(int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.memo.MemoForIndex
getMemoForMark(Mark) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
getMemoForMark(MarkCollection, Mark) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
getMemoized() - Method in class org.anchoranalysis.io.manifest.finder.FinderSerializedObject: Provides a memoized (cached) means of access the results of the finder
getMerge() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
getMerged() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects: Returns a merged version of the two-objects available (or null if not available)
getMergedOptional() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
getMergedPosTolerance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
getMergeMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
getMessage() - Method in exception org.anchoranalysis.core.index.GetOperationFailedException
getMessage() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
getMessageLogger() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful: Exposed as StatefulMessageLogger rather than as MessageLogger that is found in Logger
getMessageReporter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: The associated message reporter.
getMethod() - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
getMethod() - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ: One of the following strings to identify ImageJ's thresholding algorithms (or an empty string for the default).
getMiddlePoint() - Method in class org.anchoranalysis.spatial.Contour
getMin() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
getMin() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
getMin() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
getMin() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
getMin() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
getMin() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Minimum-boundary for acceptable range
getMin() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
getMin() - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
getMin() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature: Calculates minimally-allowed range boundary
getMin() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars: Boundary value indicating minimally-allowed range value
getMin(Function<FileDetails, Optional<Integer>>) - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
getMinConfidence() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum confidence of an element for its object-mask to be included.
getMinConfidence() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText: Proposed bounding boxes below this confidence interval are removed
getMinDiff() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
getMinDifference() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: A minimum difference, below which 0.0 is returned
getMinDifference() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
getMinDiversity() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMinimaImposition() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
getMinimumBoundingBoxVolume() - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel: Only objects whose bounding-box volume is greater or equal to this threshold are included.
getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
getMinimumIndex() - Method in interface org.anchoranalysis.core.index.bounded.BoundedRange
getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
getMinIntensity() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
getMinIntensity() - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D: Intensity for thresholding
getMinIntensityValue() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
getMinMaxIgnoreBeforeIndex() - Method in class org.anchoranalysis.plot.index.LinePlot
getMinNumberObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
getMinNumberPoints() - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints: If a contour has less than this number of points, we don't split it, and return it as-is
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares: Only includes squares that have at lesat this number of voxels
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum number of voxels that must exist in a connected-component to be included.
getMinNumPoints() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
getMinNumPoints() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: If an object has fewer points than before being fitted, we ignore
getMinNumSlices() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
getMinNumZSlices() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
getMinorAxisAngle() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
getMinorAxisSlope() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
getMinOverlap() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
getMinRadius() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
getMinRadius() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
getMinRadScaleEnd() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
getMinRadScaleStart() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
getMinRatio() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
getMinRatioPointsInsideRegion() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
getMinSize() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
getMinusOne() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
getMinVal() - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
getMinVolume() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
getMinVolume() - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
getMinVolumeConnectedComponent() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
getMinX() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Minimum X coordinate inclusive
getMinXYRes() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
getMinY() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Minimum Y coordinate inclusive
getMinZ() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Minimum Z coordinate inclusive
getModelDirectory() - Method in class org.anchoranalysis.core.log.CommonContext: Directory where machine-learning models can be found
getModelDirectory() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
getModelDirectory() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
getModelDirectory() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
getModelDirectory() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: An input-directory in which models are stored.
getModelDirectory() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
getModelPool() - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
getMultipleComparer() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
getMultiplyBy() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
getName() - Method in class org.anchoranalysis.bean.define.adder.FromXmlList: The name of the file in the current working directory WITHOUT THE .xml EXTENSION
getName() - Method in class org.anchoranalysis.bean.NamedBean: The name associated with item
getName() - Method in class org.anchoranalysis.bean.shared.path.RootPath
getName() - Method in interface org.anchoranalysis.core.identifier.name.NameValue: The associated name
getName() - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
getName() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
getName() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue: An optional-name.
getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
getName() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath: A unique name associated with the path
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
getName() - Method in class org.anchoranalysis.mpp.mark.Mark
getName() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
getName() - Method in class org.anchoranalysis.mpp.mark.points.PointList
getName() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
getName() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
getName() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
getName() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
getName() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
getName() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
getName() - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile: A name to describe the adjacent file
getName() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase: The name of the appended entity
getName(S) - Method in interface org.anchoranalysis.bean.permute.ApplyPermutations.NameGetter
getNamedFilePathCollection() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsInitParams
getNamedKeyValueParamsCollection() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsInitParams
getNameLeft() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
getNamer() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: Assigns each input a unique compact name.
getNameRight() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
getNames() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
getNames() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
getNameValueSet() - Method in class org.anchoranalysis.overlay.OverlayProperties
getNavigateHigherDirs() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: Search x number directories higher than file
getNoProposalReason() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
getNumberChannels() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.Stack
getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
getNumberChannels() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
getNumberChannels() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
getNumberColors() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
getNumberDilations() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
getNumberFrames() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
getNumberFrames() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
getNumberGPUProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: How many GPU processors to use when this is possible as a substitute for a CPU processor
getNumberKernels() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
getNumberLoopPoints() - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
getNumberPoints() - Method in class org.anchoranalysis.plot.index.LinePlot
getNumberSeries() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
getNumberSlices() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
getNumberSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories: How many directories to include in the name.
getNumBins() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The number of bins in each histogram for a cell
getNumCols() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
getNumColsUsed() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
getNumDecimalPlaces() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
getNumDim() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
getNumLeadingZeros() - Method in class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
getNumLevelsGrouping() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
getNumMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
getNumRep() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
getNumRep() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
getNumRows() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
getNumRowsUsed() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
getObject() - Method in class org.anchoranalysis.annotation.io.image.findable.Found: The found object
getObject() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
getObject() - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
getObject() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
getObject() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
getObject() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
getObject1() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
getObject2() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
getObjectMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each intermediary-object to a final-object
getObjects() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
getObjects() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
getObjects() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
getObjects() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: The objects for whom a level is calculated
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects: Objects to draw on a background
getObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
getObjects() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection: The objects in the collection.
getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
getObjects() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
getObjects() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
getObjects() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.

What's allowed or not when outputting object-collections
getObjects() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
getObjects() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
getObjects1() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: First collection with items to be merged
getObjects2() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: Second collection with items to be merged
getObjectsBlue() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
getObjectsContainer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
getObjectsElse() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
getObjectsGreater() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
getObjectsGreen() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
getObjectsGrouped() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
getObjectsLesser() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
getObjectsRed() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
getObjectsRejected() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
getObjectsSave() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Saves all objects that are inputs to the merge, outputs from the merge, or intermediate merges along the way
getObjectsSeeds() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
getObjectsSeeds() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
getObjectsSource() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
getObjectsSource() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
getObjectsSplitBy() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
getObjectsTarget() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
getOffByte() - Method in class org.anchoranalysis.image.core.mask.Mask
getOffByte() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: The byte representation of the value for OFF
getOffInt() - Method in class org.anchoranalysis.image.core.mask.Mask
getOffInt() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues: The integer representation of the value for OFF
getOnByte() - Method in class org.anchoranalysis.image.core.mask.Mask
getOnByte() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: The byte representation of the value for ON
getOnInt() - Method in class org.anchoranalysis.image.core.mask.Mask
getOnInt() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues: The integer representation of the value for ON
GetOperationFailedException - Exception in org.anchoranalysis.core.index: When a get operation fails for a particular key
GetOperationFailedException(int, String) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
GetOperationFailedException(int, Throwable) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
GetOperationFailedException(Exception) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
GetOperationFailedException(String, String) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
GetOperationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
getOptimization() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: The optimization-scheme that determines which configurations are accepted/rejected from one iteration to the next.
getOptional(String) - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider: Retrieves the item if it exists, or returns empty() if it doesn't exist.
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
getOptional(String) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
getOptional(String) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
getOptional(String) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequence
getOptional(String) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
getOptional(String) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapTimeSequenceAsStack
getOptionList() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
getOptions() - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
getOptions() - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
getOrCalculate(T) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T, U) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap
getOrCalculate(T, U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCreate(Class<?>) - Method in class org.anchoranalysis.core.identifier.provider.store.SharedObjects: Gets an existing store, or creates a new one
getOrCreateNew(K) - Method in class org.anchoranalysis.core.identifier.name.MapCreate
getOrientation() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
getOrientation() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
getOrientationProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
getOrientationXYProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
getOriginal() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject: Original unscaled element before any operations
getOrNull(U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap: Gets an existing result for the current params from the cache.
getOutlineColor() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The color of the outline
getOutlinePixelsRetriever() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
getOutlinePixelsRetrieverReverse() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
getOutlineProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
getOutlineWidth() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The width of the outline (only relevant if outline==true
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: The width of the outline.
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The width of the outline
getOutlineWidth() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
getOutlineWidth() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
getOutPath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: Constructs a path as an output, replacing $1, $2 etc.
getOutPathPrefix() - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: A directory in which to output the experiment-directory and files
getOutput() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: The output-manager that specifies how/where/which elements occur duing outputting.
getOutput() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
getOutput() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
getOutputDirectory() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments: A directory indicating where inputs can be located
getOutputDirectory() - Method in class org.anchoranalysis.io.output.path.prefixer.FilePathPrefixerContext: A directory indicating where inputs can be located
getOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.

What's allowed or not - highest level outputs
getOutputEnabled() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
getOutputEnabledDelta() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments: Additions/subtractions of outputs for the experiment supplied by the user.
getOutputFolderPath() - Method in class org.anchoranalysis.io.output.outputter.Outputter
getOutputFolderPath() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
getOutputName() - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileBase: The name to use (without extension) for the text-file log
getOutputName() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata: The output name for the features CSV.
getOutputName() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
getOutputName() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
getOutputName() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: An identifier used in rules to determine if an output is enabled or not.
getOutputName() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
getOutputName() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
getOutputName() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
getOutputName() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
getOutputNameStyle() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
getOutputNameStyle() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
getOutputPattern() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
getOutputRGBOutline() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
getOutputRGBOutlineFlattened() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
getOutputsDisabled() - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled: The names of the outputs that are disbled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled: The names of the outputs that are enabled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.bean.OutputManager: Which outputs are enabled or not enabled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Which outputs are enabled or not enabled.
getOutputStackProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
getOutputter() - Method in class org.anchoranalysis.experiment.task.InputBound
getOutputter() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
getOutputter() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
getOutputter() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter: The outputter to be used for the sequence.
getOutputter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: An outputter that writes to the particular output-directory.
getOutputter() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
getOutputterFor(String) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: groupIdentifierFor should always called at least once before getOutputManagerFor
getOutputWriteSettings() - Method in class org.anchoranalysis.io.output.bean.OutputManager: General settings (default file extensions, colors etc.) for outtping files.
getOutputWriteSettings() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
getOutside() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies otside the range
getOverlapRatioThreshold() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
getOverlapThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects: The maximum size for merging.
getOverlays() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
getOverlays() - Method in class org.anchoranalysis.overlay.IndexableOverlays
getPadding() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase: Padding placed on each side of the outputted image (if it's within the image)
getPaddingXY() - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in XY directions
getPaddingZ() - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in Z direction
getPair() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
getPair() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
getPair() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Every combination of interactions between marks and the associated energy
getPairAddCriteria() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
getPairAddCriteria() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
getPairCollection() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
getPairsFor(Mark) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
getPairTypeClass() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
getParametersExperiment() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
getParamMean() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
getParamPrefix() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
getParams() - Method in class org.anchoranalysis.feature.energy.EnergyStack
getParams() - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
getParams() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
getParams() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getParams() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
getParams() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
getParams() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getParams() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getParams() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
getParams() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
getParams() - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
getParams() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
getParams() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
getParams() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor: Parameters used for calculating HOG
getParams() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: Parameters used for calculating HOG
getParamsOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
getParamsOptional() - Method in interface org.anchoranalysis.feature.input.FeatureInputParams
getParamsOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
getParamsRequired() - Method in interface org.anchoranalysis.feature.input.FeatureInputParams
getParamStdDev() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
getParent() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
getParentDirectoryCreator() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
getParentFolder() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
getParentFolder() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
getParentOutputter() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
getPartition() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition
getPath() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: Path to annotation
getPath() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound: the path an object was not found at.
getPath() - Method in class org.anchoranalysis.bean.shared.path.RootPath: A path on a filesystem to the directory, that defines the root
getPath() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath: The path
getPath() - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
getPath() - Method in class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
getPathAnnotation() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
getPathDefaultMarks() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
getPathLabel() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller: Path to a CSV label file (comma-separated, with header, no quotes)
getPathParams() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
getPaths() - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles: All files need to be present
getPaths() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
getPayload() - Method in class org.anchoranalysis.core.graph.TypedEdge: The edge.
getPayload() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
getPenaltyValue() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
getPeriodTriggerBank() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
getPermutation() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A permutation to apply.
getPermutations() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A list of permutations to apply.
getPermuteProperty() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
getPermuteProperty() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
getPermuteProperty() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
getPixelsForPlane(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
getPlotBackgroundColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
getPlotGridlineColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
getPlusOne() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
getPoints() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getPoints() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
getPoints() - Method in class org.anchoranalysis.spatial.Contour
getPointsFitter() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
getPointsFitter() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Name of the PointsFitter to use.
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
getPointsFitterSet() - Method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
getPointsFromOrientationProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
getPointsFromOrientationXYProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
getPointsProposer() - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
getPos() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
getPositionProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
getPositionProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
getPower() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
getPrefix() - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean: A prefix that is placed before the name of every bean created
getPrefix() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
getPrefix() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
getPrefix() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
getPrefix() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
getPrefixer() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: The OutputManager associated with the experiment which Outputter uses.
getPrependColor() - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend
getPrependString() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
getPrependString() - Method in class org.anchoranalysis.feature.bean.list.PrependName
getPrependString() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
getPrependString() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
getPriority() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
getProbMapID() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
getProbMapSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getProbNeg() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
getProbPos() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
getProperties() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
getProperty(String) - Method in class org.anchoranalysis.core.value.KeyValueParams
getProperty(String) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
getPropertyAsDouble(String) - Method in class org.anchoranalysis.core.value.KeyValueParams
getPropertyDefiner() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
getPropertyInitializer() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
getPropertyPath() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath: Either a direct property of a bean e.g.
getProposal() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
getProposal() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
getProposalSecondary() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting: An optional additional marks-Energy that provides an additional explanation of proposed
getProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
getProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
getProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
getPxlPartMemo() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
getPxlPartMemo() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
getQuantile() - Method in class org.anchoranalysis.feature.bean.results.Quantile: The quantile.
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
getQuantileHigh() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
getQuantileLow() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
getQuantileLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
getQuantileUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
getRadii() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
getRadii() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
getRadiiProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
getRadiiProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
getRadius() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
getRadius() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
getRadius() - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
getRadius() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
getRadiusBound() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
getRadiusBound() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
getRadiusX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
getRadiusY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
getRadiusZ() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
getRandomNumberGenerator() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
getRangeAxisLimits() - Method in class org.anchoranalysis.plot.PlotInstance
getRangeC() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
getRangeT() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
getRangeZ() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
getRate() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Gets an unsigned-byte (represented as a byte) at the current buffer position.
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as an int) at the current buffer position.
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Gets an unsigned-short (represented as a short) at the current buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Gets an unsigned-byte (represented as a byte) at a particular buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as a int) at a particular buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Gets an unsigned-short (represented as a short) at a particular buffer position.
getReason() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
getReceive() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
getRecordedOutputs() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: If defined, records output-names that are written / not-written during the experiment.
getRed() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
getRed() - Method in class org.anchoranalysis.core.color.RGBColor
getRed() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
getReduce() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: Method for reducing all pairs into a single value e.g.
getReduce() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima: The algorithm for reducing the number of object-masks.
getReferencePoissonIntensity() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
getReferencesFeatureListCreator() - Method in class org.anchoranalysis.feature.bean.list.ReferencedFeatures: Ensures any feature-lists mentioned here are evaluated, before this list is created.
getReferencesFeatureListCreator() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: Makes sure a particular feature list creator is evaluated
getRegex() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
getRegex() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: Regular expression to match against string
getRegex() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: A regular-expression applied to the image file-path that matches three groups.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx: Regular expression to use to match path with at least one group in it.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: The regular-expression to use for matching groups.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching: If a path matches a regular expression it is removed.
getRegEx() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
getRegexAdjacent() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: This needs to be set if there is at least one adjacentChannel.
getRegExDir() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to directories
getRegExFile() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to files
getRegion() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
getRegion() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
getRegionID() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
getRegionID() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.FeatureMarkRegion
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
getRegionID() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
getRegionMap() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
getRegionMap() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
getRegionMap() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
getRegionMap() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
getRegionMap() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
getRegionMap() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
getRegionMembership() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
getRejectionReason() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
getRelation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
getRelation() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
getRelation() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Relation to threshold
getRelation() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
getRelation() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
getRelation() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
getRelation() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
getRemainder() - Method in class org.anchoranalysis.core.system.path.SplitPath
getRepeat() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
getRepeats() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth: Total number of births
getReplacement() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
getReplacement() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: What to replace in the path
getReplacement() - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile: The replacement string used to determine the file
getRequireArguments() - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf: The conditions that must be fulfilled
getRequireArguments() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
getResizeTo() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask: If set, each channel is scaled to a specific size before the mean is calculated (useful for combining different sized images)
getResizeTo() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor: The input-image is rescaled to this width/height before calculating HOG descriptors
getResizeTo() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: The input is rescaled to this width/height before calculating HOG descriptors
getResolution() - Method in class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
getResolutionOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
getResolutionOptional() - Method in interface org.anchoranalysis.feature.input.FeatureInputWithResolution
getResolutionOptional() - Method in class org.anchoranalysis.image.feature.histogram.FeatureInputHistogram
getResolutionOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
getResolutionOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
getResolutionRequired() - Method in interface org.anchoranalysis.feature.input.FeatureInputWithResolution
getRestrictTo() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If set, the inversion only occurs on a particular region of the mask, as determined by this mask
getResults() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
getResultsVector() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
getResX() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
getResY() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
getResZ() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
getReverse() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
getRGB() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
getRGB() - Method in class org.anchoranalysis.core.color.RGBColor
getRight() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare: Objects on right-side of the comparison
getRoot() - Method in class org.anchoranalysis.core.system.path.SplitPath
getRoot() - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
getRoot() - Method in class org.anchoranalysis.test.TestLoader
getRoot1() - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
getRoot2() - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
getRootFolder() - Method in class org.anchoranalysis.io.manifest.Manifest
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
getRootName() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: If non-empty then a rooted filesystem is used with this root
getRootName() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: Root-name assuming multi-rooted strucutre
getRootName() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
getRootNameForStructure() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: If rootInStructure==true, the rootName is placed in the folder structure.
getRootPath() - Method in class org.anchoranalysis.plugin.io.manifest.DeserializedManifest
getRotationAngle() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
getRotationAngle() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
getRotationBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
getRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
getRotationX() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
getRotationY() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
getRotationZ() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
getRotMatrix() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
getRow() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
getRow(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
getRowForListIndex(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
getRowSource() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
getSampleEvery() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
getScalarProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
getScalarProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
getScale() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic: Standard-Deviation
getScale() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Whether to increase or reduce the size of the images
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY: Determines how much to scale by
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
getScaleCalculator() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
getScaleFactor() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
getScaleLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity: Sets the min by multiplying the quantileLower by this constant.
getScaleLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
getScaleRadii() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
getScaleUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity: Sets the max by multiplying the quantileUpper by this constant.
getScaleUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
getScore() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
getScoreProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
getScoreThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression: Bounding boxes with scores above this threshold are removed
getSearchObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
getSecond() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
getSecond() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
getSecond() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the second-level (for all first level output-names)
getSecond() - Method in class org.anchoranalysis.mpp.segment.transformer.Compose: Second transformation from U to T
getSecondary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
getSegment() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
getSegment() - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: Segmentation algorithm
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The segmentation procedure.
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
getSegment() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The segmentation algorithm
getSegment() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage: How to perform the segmentation.
getSegment() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima: The segmentation algorithm that is applied as an input to non-maxima suppression.
getSegmentStack() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
getSelect() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair: Either "merged" or "first" or "second" indicating which feature to delegate from
getSelectChannels() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Selects which channels are included, optionally renaming.
getSemiMajorAxis() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
getSemiMinorAxis() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
getSeperator() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
getSeperator() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
getSequence() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence: Where the sequence starts
getSequence() - Method in class org.anchoranalysis.feature.bean.list.ListSequence: First number range that is appended
getSequence() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
getSequenceAdditional() - Method in class org.anchoranalysis.feature.bean.list.ListSequence: Another number range that is appended
getSequenceType() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed
getSequenceType() - Method in class org.anchoranalysis.io.manifest.ManifestDirectoryDescription: A sequence-type to describe the different filenames outputted in the directory.
getSeriesColors() - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
getSeriesNameFor(int) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
getSet() - Method in class org.anchoranalysis.feature.shared.SharedFeatureSet
getSetPoints() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
getSettings() - Method in class org.anchoranalysis.io.output.outputter.Outputter
getSettings() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: General settings for writing outputs.
getSharedFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
getSharedFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
getSharedFeatureSet() - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
getSharedObjects() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
getSharedObjects() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
getSharedState() - Method in class org.anchoranalysis.experiment.task.InputBound
getSharedState() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
getShellRad() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
getShellRad() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
getShellRad() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
getShellRad() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
getShellRad() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
getShellRad() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
getShellRad() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
getShift() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
getShortTitle() - Method in class org.anchoranalysis.plot.bean.Plot: A shortened version of Plot.getTitle().
getShowOngoingJobsLessThan() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: When the number of ongoing jobs is less than this threshold, they are shown in event logs.
getSigma() - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
getSigma() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
getSimplePairCollection() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
getSimplePairCollectionID() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
getSingle() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
getSize() - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
getSize() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
getSize() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram: Size of the image produced showing a plot of the histogram
getSize() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Size of all created thumbnails
getSize() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
getSize() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
getSize() - Method in class org.anchoranalysis.plugin.io.multifile.IntegerRange
getSizeHalf() - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
getSkipFirstTrim() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
getSkipFirstTrim() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
getSkipNumberSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories: Initially skip this number of directories before including them in the description.
getSlice() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
getSlice(int) - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
getSlice(int) - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
getSliceEnd() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
getSliceFirst() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: First slice.
getSliceID() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase: Index of slice to use, or -1 to use all slices
getSliceIndex() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Which slice to use from mask
getSliceLast() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Last slice.
getSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getSliceStart() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
getSmoothingFactor() - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
getSource() - Method in class org.anchoranalysis.bean.shared.StringMapItem
getSource() - Method in class org.anchoranalysis.image.core.object.MatchedObject: The source object (which is matched against others)
getSource() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
getSource() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
getSource() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Source of feature-values to be exported
getSource() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.DualVoxelizedMarks
getSource() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
getSourceFolderPath() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
getSplitDescriptiveNameRegex() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
getSplitProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
getSquareSize() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
getStack() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
getStack() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
getStack() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
getStack() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
getStack() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Provides a stack.
getStack() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The stack to segment
getStack() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV: The stack that is the background for our objects
getStackEnergy() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Optionally specifies an energy-stack to be associated with every calculation input.
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks)
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
getStackEnergy() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
getStackID() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
getStackName() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One: If defined, processing only occurs the stack with this specific stack and index.
getStackNameVisualOriginal() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
getStackProviderID() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Specifies the ID of an existing stack.
getStackProviderID() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
getStackReader() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
getStackReader() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
getStackReader() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
getStackReader() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
getStackReader() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
getStackReader() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: The raster-reader for reading the main file
getStackReaderAdjacent() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: The raster-reader to use for opening any adjacent-channels
getStackReaderAppend() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: The raster-reader for reading any appended files
getStackReaderHigh() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
getStackReaderInput() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
getStackReaderLow() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
getStackReaderMiddle() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
getStacksOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.

What's allowed or not when outputting stacks
getStacksOutputEnabled() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
getStackStore() - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
getStart() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: The index to begin iteration from
getStartIndex() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
getStartingIntensity() - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel: The first intensity-value to consider as a valid object (e.g.
getStartPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
getState() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
getStateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
getStrategy() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
getStrategy() - Method in class org.anchoranalysis.feature.session.strategy.replace.bind.BoundReplaceStrategy
getStrategy() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
getSubdirectory() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: If non-empty than an additional subdirectory is appended as a suffix ${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
getSubDirectory() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
getSubdirectoryName() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern: The name of a subdirectory in the current context to write to, or if empty, files are written into the current directory context.
getSubtractConstant() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
getSubtractRadii() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
getSuffix() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
getSum() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: The running sum
getSummarizer() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
getSummarizer() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
getSummarizerElse() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) <= countThreshold
getSummarizerGreaterThan() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) > countThreshold
getTarget() - Method in class org.anchoranalysis.bean.shared.StringMapItem
getTask() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
getTask() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
getTask() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
getTask() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
getTask() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
getTask() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
getTaskName() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments: A name to describe the ongoing task
getTaskProcessor() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: What task is associated with the experiment, and how it is processed.
getTemperature() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
getTemperature() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
getTemplateMark() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
getTemporary() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
GetterFromIndex<T> - Interface in org.anchoranalysis.core.index
getTermination() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
getThreshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold: Only considers values greater or equal to the threshold
getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
getThreshold() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
getThresholder() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
getThresholder() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold: The thresholder that will convert a channel into a binary-channel
getThresholdHigh() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
getThresholdLow() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
getThumbnail() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Generates a thumbnail representation of one or more objects combine, as form a single input
getThumbnail() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Method to generate a thumbnail for images
getThumbnail() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
getThumbnailBatch() - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
getTime() - Method in class org.anchoranalysis.experiment.task.processor.JobState
getTimeAnnotationLastUpdated() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Number of seconds since the UNIX epoch
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getTimeIndexGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
getTimes() - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat
getTitle() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
getTitle() - Method in class org.anchoranalysis.plot.bean.Plot: The full title of the plot.
getTitle() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
getTo() - Method in class org.anchoranalysis.core.graph.TypedEdge: The vertex the edge joins to.
getToleranceLog10() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
getTotal() - Method in class org.anchoranalysis.feature.energy.EnergyTotal
getTotal() - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
getTotalCount() - Method in class org.anchoranalysis.math.histogram.Histogram
getTotalNumberTasks() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
getTransformer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
getTransformer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
getTransformer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
getTransformerKernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
getTransformerMarks() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
getTransformerPrimary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
getTransformerSecondary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
getTransformerStateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
getTriggerTerminationCondition() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
getTrimTrailingDirectory() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
getTrimTrailingDirectory() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
getType() - Method in class org.anchoranalysis.io.manifest.ManifestDescription: Identifies the type of entity.
getUnconvertedVoxelAt(int, Point3i) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
getUniqueLabel() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Label that uniquely identifies the ID (for machine purposes)
getUnit() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
getUnit() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
getUnitConverterOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
getUnitType() - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
getUnitType() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
getUnitTypeFrom() - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
getUnitTypeTo() - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
getUnitValueDistance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Gets an unsigned-byte (represented as a int) at the current buffer position.
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as a long) at the current buffer position.
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Gets an unsigned-byte (represented as a int) at a particular buffer position.
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as a long) at a particular buffer position.
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
getUnsignedByte() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
getUnsignedInt() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
getUnsignedShort() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
getUsageFooter() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
getUsageHeader() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
getUserFriendlyLabel() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Descriptive user-friendly label displayed via GUI
getValue() - Method in class org.anchoranalysis.bean.NamedBean
getValue() - Method in interface org.anchoranalysis.core.identifier.name.NameValue: The associated value
getValue() - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
getValue() - Method in class org.anchoranalysis.core.value.TypedValue
getValue() - Method in class org.anchoranalysis.feature.bean.operator.Constant
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
getValue() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue: The value.
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
getValue() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
getValue() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getValue() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
getValue() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
getValue() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
getValue() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
getValue() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
getValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
getValueIfEmpty() - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic: The value to return iff exceptionifEmpty is false
getValueIfTooFewVoxels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: A value to return if there are too few voxels (less than MIN_NUM_VOXELS to calculate moments
getValueNoObject() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
getValueNoObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
getValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
getValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet: The values of the string-set
getVersion() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
getVersionFooter() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
getVertex() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
getVerticalAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
getVisitScheduler() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
getVoxelDataType() - Method in class org.anchoranalysis.image.core.channel.Channel
getVoxelDataType() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
getVoxels() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
getVoxelsConverter() - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter
getWeight() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
getWeight() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
getWeightBackground() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
getWeightedKernelFactory(int) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
getWeightForeground() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
getWeightItem1Greater() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
getWeightItem2Greater() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
getWeightNegative() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
getWeightNegative() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
getWeightNegative() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
getWeightPositive() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
getWeightPositive() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
getWeightPositive() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
getWeightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
getWhenDetailed() - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging: Logger to use when detailed-logging is on
getWhenEqual() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getWhenNot() - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging: Logger to use when detailed-logging is off
getWhenNotEqual() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
getWhenOneOrThreeChannels() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a one or three-channeled image, that is not 3D, and not RGB.
getWhenRGB() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a three-channeled RGB image and is not 3D.
getWidth() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
getWidth() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Width (what the difference is divided by)
getWidthFactor() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
getWindowSize() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
getWindowSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The window-size as per OpenCV implementation.
getWithin() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies within the range
getWithinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange: Constant to return if value lies within the range
getWithinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature: Constant to return if value lies within the range
getWriter() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
getWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Default writer, if a more specific writer is not specified for a condition.
getWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
getWriterAlways2D() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Writer to use if it is guaranteed that the image will always be 2D.
getWriterElse() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Otherwise the writer to use.
getWriterInstance(Class<?>) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: Gets a writer-instance for a particular writerParentClass.
getWriters() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
getWriters() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: The writers associated with this output-manager.
getX() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
getX() - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
getXMax(Point3i, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
getXMin(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
getXmlAggregatedGroup() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames: The name of the XML file outputted with aggregated values for each group, if enabled.
getXMLConfiguration() - Method in class org.anchoranalysis.experiment.bean.Experiment
getY() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
getY() - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
getYAxisLowerMargin() - Method in class org.anchoranalysis.plot.index.LinePlot
getYAxisUpperMargin() - Method in class org.anchoranalysis.plot.index.LinePlot
getYMax(Point3i, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
getYMin(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
getYVal(T, int) - Method in interface org.anchoranalysis.plot.index.LinePlot.YValGetter
getYValGetter() - Method in class org.anchoranalysis.plot.index.BarPlot
getYValGetter() - Method in class org.anchoranalysis.plot.index.LinePlot
getZ() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
getZAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
getZSliceGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
getZSliceNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
getZSliceNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
getZSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
GlobalRegionIdentifiers - Class in org.anchoranalysis.mpp.mark
GradientBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
GradientBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
GradientBaseAddSum - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
GradientBaseAddSum() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
gradientCalculation() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
GradientForAxis - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Extracts the gradient in the direction of a particular axis (identified by an index)
GradientForAxis() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
GradientMagnitude - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
GradientMagnitude() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMagnitude
GradientMeanForAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
GradientMeanForAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
GradientXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Gradient in x and y axes
GradientXY() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientXY
GraphLogger - Class in org.anchoranalysis.plugin.image.object.merge
GraphLogger(DescribeGraph, Logger) - Constructor for class org.anchoranalysis.plugin.image.object.merge.GraphLogger
GraphWithoutPayload<V> - Class in org.anchoranalysis.core.graph: A graph, either directed or undirected, where edges contain no payload.
GraphWithoutPayload(boolean) - Constructor for class org.anchoranalysis.core.graph.GraphWithoutPayload: Creates the graph.
GraphWithPayload<V,P> - Class in org.anchoranalysis.core.graph: A graph, either directed or undirected, with edges containing a payload of type E.
GraphWithPayload(boolean) - Constructor for class org.anchoranalysis.core.graph.GraphWithPayload: Creates the graph.
GrayscaleReconstruction2DIJ - Class in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
GrayscaleReconstruction2DIJ() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction.GrayscaleReconstruction2DIJ
GrayscaleReconstructionByErosion - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
GrayscaleReconstructionByErosion() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionByErosion
GrayscaleReconstructionRobinson - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
GrayscaleReconstructionRobinson() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionRobinson
greaterEqualThan(VarianceCalculator) - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
GreaterIntersectionWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only accepts an object if it has greater (or EQUAL) intersection with objectsGreater than objectsLesser
GreaterIntersectionWith() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
GreaterThan - Class in org.anchoranalysis.math.relation
GreaterThan() - Constructor for class org.anchoranalysis.math.relation.GreaterThan
GreaterThanBean - Class in org.anchoranalysis.bean.shared.relation
GreaterThanBean() - Constructor for class org.anchoranalysis.bean.shared.relation.GreaterThanBean
GreaterThanEqualTo - Class in org.anchoranalysis.math.relation
GreaterThanEqualTo() - Constructor for class org.anchoranalysis.math.relation.GreaterThanEqualTo
GreaterThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation
GreaterThanEqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
GreaterThanThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the threshold
GreaterThanThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
GreatestAreaSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
GreatestAreaSlice() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
greedyMatch() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Find a valid matching by greedily selecting among zero-cost matchings.
green() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
GroupedAnnotationLabels - Class in org.anchoranalysis.plugin.annotation.bean.label: A set of annotation labels partitoned into their unique groups
GroupedAnnotationLabels(Collection<AnnotationLabel>) - Constructor for class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
groupedLabels() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
GroupedMeanChannelTask - Class in org.anchoranalysis.plugin.image.task.bean.grouped.raster: Creates a an aggregated-image for each group, where each voxel-value is the mean voxel-value across the group.
GroupedMeanChannelTask() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
GroupedSharedState<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped: Commonality between shared state for gouped export tasks
GroupedSharedState(Function<ConsistentChannelChecker, GroupMapByName<S, T>>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState
GroupedStackBase<S,T> - Class in org.anchoranalysis.plugin.image.task.bean.grouped: Base class for stacks (usually each channel from an image) that are somehow grouped-together.
GroupedStackBase() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
GroupFiles - Class in org.anchoranalysis.plugin.io.bean.groupfiles: An input-manager that can group together files to form stacks or time-series based on finding patterns in the file path (via regular expressions)
GroupFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
GroupingRoot - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a set of definitions of classes can be collectively grouped using this class.
GroupMapByName<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped: Adds items to aggregate structures identified uniquely by a name, and allows these items to be later outputted.
GroupMapByName(String, String, Supplier<T>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName: Creates a group-map.
groupNameSet() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.IndexedCSVRows
GroupWriter - Class in org.anchoranalysis.feature.io.results.group: Writes outputs pertaining to groups to the filesystem.
GroupWriter(ResultsWriterMetadata) - Constructor for class org.anchoranalysis.feature.io.results.group.GroupWriter
growBuffer(Point3i, Point3i, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
growBuffer(Point3i, Point3i, Optional<Extent>, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Grows buffer of the object-mask in positive and negative directions by a certain amount.
growBy(int) - Method in class org.anchoranalysis.spatial.Extent
growBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
growBy(Tuple3i, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
growToZ(int) - Method in interface org.anchoranalysis.image.core.object.seed.Seed
growToZ(int) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
growToZ(int) - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
growToZ(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
growToZ(int, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
guaranteedImageAttributes() - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
GuessDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider: Guesses dimensions from the input-image if it exists.
GuessDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.GuessDimensions

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has(int) - Method in interface org.anchoranalysis.core.color.ColorIndex
has(int) - Method in class org.anchoranalysis.core.color.ColorIndexModulo
has(int) - Method in class org.anchoranalysis.core.color.ColorList
has(int) - Method in class org.anchoranalysis.core.color.SingleColor
has(K) - Method in class org.anchoranalysis.core.cache.LRUCache
has(T) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti: Checks whether the cache contains a particular input already.
hasAboveZero() - Method in class org.anchoranalysis.math.histogram.Histogram
hasAllRequiredArguments(boolean) - Method in class org.anchoranalysis.experiment.bean.require.RequireArguments
hasAllRequiredArguments(boolean) - Method in class org.anchoranalysis.experiment.bean.require.RequireDebugMode
hasArray() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Whether the buffer has an array?
hasAtLeastOneDisabled() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: If there is at least one disabled output.
hasAtLeastOneDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: If there is at least one disabled output.
hasAtLeastOneEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: If there is at least one enabled output.
hasAtLeastOneMultiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Multiplex between RecordedOutputs.hasAtLeastOneEnabled() and RecordedOutputs.hasAtLeastOneDisabled().
hasBeenInit() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
hasBeenInitialized() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
hasCachedCalculation() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
hasChannel(String) - Method in class org.anchoranalysis.plugin.image.task.channel.ChannelGetterForTimepoint
hasColorGetter() - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
hasEqualXAndY() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
HasFriendlyErrorMessage - Interface in org.anchoranalysis.core.exception.friendly: Methods for extracting a user-friendly error description
hashCode() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
hashCode() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
hashCode() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
hashCode() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
hashCode() - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization
hashCode() - Method in class org.anchoranalysis.bean.shared.path.RootPath
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
hashCode() - Method in class org.anchoranalysis.core.color.RGBColor
hashCode() - Method in class org.anchoranalysis.core.concurrency.WithPriority
hashCode() - Method in class org.anchoranalysis.core.graph.TypedEdge
hashCode() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
hashCode() - Method in class org.anchoranalysis.core.index.Indexable
hashCode() - Method in class org.anchoranalysis.core.log.CommonContext
hashCode() - Method in class org.anchoranalysis.core.system.path.SplitPath
hashCode() - Method in class org.anchoranalysis.core.value.TypedValue
hashCode() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap
hashCode() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
hashCode() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
hashCode() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputNull
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
hashCode() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
hashCode() - Method in class org.anchoranalysis.feature.io.name.CombinedName
hashCode() - Method in class org.anchoranalysis.feature.io.name.SimpleName
hashCode() - Method in class org.anchoranalysis.feature.results.ResultsVector
hashCode() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
hashCode() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
hashCode() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
hashCode() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
hashCode() - Method in class org.anchoranalysis.image.core.mask.Mask
hashCode() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
hashCode() - Method in class org.anchoranalysis.image.core.object.MatchedObject
hashCode() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
hashCode() - Method in class org.anchoranalysis.image.core.orientation.Orientation
hashCode() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
hashCode() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
hashCode() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
hashCode() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
hashCode() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
hashCode() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
hashCode() - Method in class org.anchoranalysis.image.core.stack.Stack
hashCode() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
hashCode() - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
hashCode() - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
hashCode() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
hashCode() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
hashCode() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
hashCode() - Method in class org.anchoranalysis.image.feature.stack.FeatureInputStack
hashCode() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
hashCode() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
hashCode() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
hashCode() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
hashCode() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
hashCode() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
hashCode() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
hashCode() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
hashCode() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
hashCode() - Method in class org.anchoranalysis.io.manifest.file.FileType
hashCode() - Method in class org.anchoranalysis.io.manifest.ManifestDescription
hashCode() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
hashCode() - Method in class org.anchoranalysis.io.output.outputter.Outputter
hashCode() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
hashCode() - Method in class org.anchoranalysis.launcher.config.HelpConfig
hashCode() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
hashCode() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
hashCode() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
hashCode() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
hashCode() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
hashCode() - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
hashCode() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
hashCode() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
hashCode() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
hashCode() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
hashCode() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
hashCode() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
hashCode() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
hashCode() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
hashCode() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
hashCode() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
hashCode() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
hashCode() - Method in class org.anchoranalysis.overlay.IndexableOverlays
hashCode() - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
hashCode() - Method in class org.anchoranalysis.overlay.Overlay
hashCode() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
hashCode() - Method in class org.anchoranalysis.plot.AxisLimits
hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
hashCode() - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
hashCode() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
hashCode() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
hashCode() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
hashCode() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
hashCode() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
hashCode() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
hashCode() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
hashCode() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
hashCode() - Method in class org.anchoranalysis.spatial.box.BoundingBox
hashCode() - Method in class org.anchoranalysis.spatial.Extent
hashCode() - Method in class org.anchoranalysis.spatial.point.Point2d
hashCode() - Method in class org.anchoranalysis.spatial.point.Point2f
hashCode() - Method in class org.anchoranalysis.spatial.point.Point2i
hashCode() - Method in class org.anchoranalysis.spatial.point.Point3d
hashCode() - Method in class org.anchoranalysis.spatial.point.Point3f
hashCode() - Method in class org.anchoranalysis.spatial.point.Point3i
hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3d
hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3f
hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3i
hashCode() - Method in class org.anchoranalysis.spatial.point.Vector3d
hashCode() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
hasIdenticalXY() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
hasInputFilterExtensions() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
hasIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
hasIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Determines whether there are any intersecting voxels on two object-masks.
hasIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingObjects: Determines whether there are any intersecting voxels on two object-masks.
hasKey(U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
hasLastDivider() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
hasMatch(String) - Method in class org.anchoranalysis.bean.shared.regex.RegEx: Returns a boolean whether the regular-expression successfully matches a string or not
hasMoreThanOneSlice() - Method in class org.anchoranalysis.image.core.stack.Stack: Does the stack have more than one slice in the z-dimension?
hasNecessaryExtents() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
hasNext() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
hasNext() - Method in interface org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement.TableCreator
hasNext() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
hasNoCombinableNestedExceptions() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException: Are there nested-exceptions (according to our traversal rules) that are combinable?
hasNoNulls() - Method in class org.anchoranalysis.feature.results.ResultsVector
hasOffVoxel() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
hasOneSlice() - Method in class org.anchoranalysis.feature.energy.EnergyStack: Does exactly one z-slice exist in the energy stack?
hasOnVoxel() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
hasOption(String) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter: Identical to CommandLine.hasOption(java.lang.String).
hasPoint(Point3f) - Method in class org.anchoranalysis.spatial.Contour
hasProperty(String) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Whether there are elements between the current position and the limit Buffer.hasRemaining().
hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Are there voxels remaining in a buffer?
hasSingleFeature() - Method in class org.anchoranalysis.feature.session.SequentialSession
hasTemporary() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
HasTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A simple scheme for counting the touching voxels.
HasTouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.HasTouchingVoxels
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: Is the execution-time of the task per-input expected to be very quick to execute?
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.experiment.bean.task.HelloWorld
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.experiment.bean.task.Task: Is the execution-time of the task per-input expected to be very quick to execute?
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
hasWrittenHeaders() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
head() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
headers() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
headers() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
headers() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
HelloWorld<S extends InputFromManager> - Class in org.anchoranalysis.experiment.bean.task: A dummy task that simply writes a message to all log files, specifically: 1.
HelloWorld() - Constructor for class org.anchoranalysis.experiment.bean.task.HelloWorld
help() - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Config for displaying help message
HelpConfig - Class in org.anchoranalysis.launcher.config
HelpConfig(String, String) - Constructor for class org.anchoranalysis.launcher.config.HelpConfig
HelperFriendlyExceptions - Class in org.anchoranalysis.bean.xml.error: Converts certain exceptions that occur from XML-Parsing into a friendly form to display to the user
HelperListUtilities - Class in org.anchoranalysis.bean.xml.factory: Utilities for manipulating list of beans
hexString() - Method in class org.anchoranalysis.core.color.RGBColor
higherCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
higherCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
higherCountExistsThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Whether the count is greater than a particular threshold.
highestConfidence() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
histogram() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
histogram() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
histogram() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
histogram() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
histogram(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
Histogram - Class in org.anchoranalysis.math.histogram
Histogram(int) - Constructor for class org.anchoranalysis.math.histogram.Histogram
Histogram(int, int) - Constructor for class org.anchoranalysis.math.histogram.Histogram
Histogram.BinConsumer - Interface in org.anchoranalysis.math.histogram: Consumers a bin and corresponding count.
HistogramFactory - Class in org.anchoranalysis.image.voxel.statistics
HistogramFixture - Class in org.anchoranalysis.test.feature.plugins
HistogramFromObjectsFactory - Class in org.anchoranalysis.image.core.object
HistogramProvider - Class in org.anchoranalysis.image.bean.provider
HistogramProvider() - Constructor for class org.anchoranalysis.image.bean.provider.HistogramProvider
HistogramProviderUnary - Class in org.anchoranalysis.image.bean.provider
HistogramProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
histograms() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
HISTOGRAMS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories: Where collections of histograms are typically placed in a define-experiment output
HistogramStatistics - Class in org.anchoranalysis.math.histogram: Further statistics that can be derived from a histogram in addition to those callable directly from the Histogram class
HistogramThresholder - Class in org.anchoranalysis.plugin.image.intensity
HOGDescriptor - Class in org.anchoranalysis.plugin.opencv.bean.feature: Creates the entire HOG descriptor for an image.
HOGDescriptor() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
HOGFeature - Class in org.anchoranalysis.plugin.opencv.bean.feature: One part of a Histogram of Oriented Gradients descriptor, as applied to an image stack.
HOGFeature() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
HOGFeature(SizeXY, int) - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
HOGParameters - Class in org.anchoranalysis.plugin.opencv.bean.feature: Parameters for calculating a HOG Descriptor covering window-size, block-size etc.
HOGParameters() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
HomeSubdirectory - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
HomeSubdirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
HorizontalCalculationCache<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.cache.horizontal: Caches CachedCalculations that occur repeatedly across many features, and store similar child caches.
HorizontalCalculationCacheFactory - Class in org.anchoranalysis.feature.session.cache.horizontal
HorizontalCalculationCacheFactory() - Constructor for class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCacheFactory
HorizontalFeatureCache<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.cache.horizontal: Caches repeated-calls to the same feature, or references to a feature by an ID-value
HorizontalFeatureCacheFactory - Class in org.anchoranalysis.feature.session.cache.horizontal
HorizontalFeatureCacheFactory() - Constructor for class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCacheFactory
HSB - Class in org.anchoranalysis.bean.shared.color.scheme
HSB() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.HSB
HungarianAlgorithm - Class in org.anchoranalysis.math.optimization: An implementation of the Hungarian algorithm for solving the assignment problem.
HungarianAlgorithm(double[][]) - Constructor for class org.anchoranalysis.math.optimization.HungarianAlgorithm: Construct an instance of the algorithm.

I

idAndIncrement() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
Identifiable - Interface in org.anchoranalysis.overlay.identifier
IdentifiablePair<T extends Identifiable> - Class in org.anchoranalysis.mpp.pair: Pair of marks
IdentifiablePair(T, T) - Constructor for class org.anchoranalysis.mpp.pair.IdentifiablePair
identifier() - Method in class org.anchoranalysis.mpp.mark.Mark
identifier() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifier: Creates an identifier for the experiment
identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
IdentifierByProperty - Class in org.anchoranalysis.image.core.object.properties
IdentifierByProperty(String) - Constructor for class org.anchoranalysis.image.core.object.properties.IdentifierByProperty
IdentifierFromMark - Class in org.anchoranalysis.mpp.mark
IdentifierFromMark() - Constructor for class org.anchoranalysis.mpp.mark.IdentifierFromMark
IdentifierFromOverlay - Class in org.anchoranalysis.overlay.identifier
IdentifierFromOverlay() - Constructor for class org.anchoranalysis.overlay.identifier.IdentifierFromOverlay
IdentifierGetter<T> - Interface in org.anchoranalysis.core.identifier.getter
IdentifierModulo<T> - Class in org.anchoranalysis.core.identifier.getter
IdentifierModulo() - Constructor for class org.anchoranalysis.core.identifier.getter.IdentifierModulo
IdentifierModulo(IdentifierGetter<T>, int) - Constructor for class org.anchoranalysis.core.identifier.getter.IdentifierModulo
IdentifyByIteration<T> - Class in org.anchoranalysis.core.identifier.getter
IdentifyByIteration() - Constructor for class org.anchoranalysis.core.identifier.getter.IdentifyByIteration
IdentifyDelegateToOverlays - Class in org.anchoranalysis.overlay.identifier
IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection) - Constructor for class org.anchoranalysis.overlay.identifier.IdentifyDelegateToOverlays
IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection, boolean) - Constructor for class org.anchoranalysis.overlay.identifier.IdentifyDelegateToOverlays
IdentifyObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score: Assigns a unique id number to each object.
IdentifyObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.IdentifyObjects
Identity - Class in org.anchoranalysis.plugin.image.feature.bean.score
Identity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.Identity
IdentityImposeValueRelationToHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.score
IdentityImposeValueRelationToHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
idFor(ObjectWithProperties, int) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: ID for a particular object
IfCondition<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.conditional: The result of featureCondition is compared to a threshold, and then either the underlying feature is calculated (positive case), or featureElse is (negative case)
IfCondition() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
IfConditionWithinRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Calculates a value if a condition lies within a certain range, otherwise returns constants
IfConditionWithinRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
IfGreaterThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Calculates a level from the first delegate and if greater than a threshold, recalculates from a second delegate.
IfGreaterThan() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
IfHighLow - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation iff first==HIGH and second==LOW then LOW voxelwise on both masks, modifying {mask} with the result.
IfHighLow() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.IfHighLow
IfKeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if a condition on key-values is satisfied otherwise maskElse is returned.
IfKeyValueCondition() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
IfLessThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Calculates a level from the first delegate and if less than a threshold, recalculates from a second delegate.
IfLessThan() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
IfNotEmpty - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if it's non-empty (at least one ON voxel) otherwise maskElse is returned.
IfNotEmpty() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfNotEmpty
IfObjectFilter - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is returned if the mask (treated as an object) passed an object-filter, otherwise maskElse is returned.
IfObjectFilter() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
IfOutsideRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: Clips a value if it lies outside the range - instead returning particular constants if below or above an acceptable range
IfOutsideRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
IfParamEqual - Class in org.anchoranalysis.plugin.image.bean.object.provider: Multiplexes between two object-collection-providers depending on whether a parameter value equals a particular string
IfParamEqual() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
IfParamEquals - Class in org.anchoranalysis.plugin.image.bean.channel.provider
IfParamEquals() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
IfPredicateBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: Base class which multiplexes between the current mask and an alternative depending if a condition is met.
IfPredicateBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
ifPresent(Optional<S>, CheckedConsumer<S, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Like Optional.map(java.util.function.Function<? super T, ? extends U>) but tolerates an exception in the mapping function, which is immediately thrown.
ifPresentSingle(String, CheckedConsumer<String, E>) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter: Executes a Consumer if an option is present.
IfStackExists - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate: The current mask is a particular stack exists (at least one ON voxel) otherwise maskElse is returned.
IfStackExists() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
IfVoxelZero - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Creates a new channel which is a merged version of two input channels according to rules.
IfVoxelZero() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
ignoreAtThreshold - Variable in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3Base: Disconsiders anything outside the threshold.
IgnoreUnderscorePrefix - Class in org.anchoranalysis.io.output.bean.enabled: All outputs are allowed unless the name's first character is an underscore.
ImageAssignLabel<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Assigns a label to each image and optionally 1.
ImageAssignLabel() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
ImageBean<T> - Class in org.anchoranalysis.image.bean
ImageBean() - Constructor for class org.anchoranalysis.image.bean.ImageBean
ImageCSVLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
ImageCSVLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
ImageCSVLabellerInitParams - Class in org.anchoranalysis.plugin.image.task.labeller
ImageCSVLabellerInitParams(FileLabelMap<String>) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
ImageFileShape - Class in org.anchoranalysis.io.bioformats.copyconvert: How to shape the image (across various dimensions) after the copying
ImageFileShape(Dimensions, int, int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
ImageInitParams - Class in org.anchoranalysis.image.bean.nonbean.init
ImageInitParams(SharedObjects) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
ImageIOWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer
ImageIOWriter() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.ImageIOWriter
ImageJRasterWriter - Class in org.anchoranalysis.io.imagej.bean.stack.writer: Base class for writing a raster using ImageJ.
ImageJRasterWriter() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
ImageLabelAnnotation - Class in org.anchoranalysis.annotation.image: A single label that pertains to an image.
ImageLabelAnnotation(String) - Constructor for class org.anchoranalysis.annotation.image.ImageLabelAnnotation
ImageLabeller<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Associates a label with an image.
ImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller
ImageLabellerStringMap<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Maps one set of labels to another
ImageLabellerStringMap() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
ImageLabellerStringMapInitParams<T> - Class in org.anchoranalysis.plugin.image.task.labeller
ImageLabellerStringMapInitParams(Map<String, String>, T) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
ImageMoments - Class in org.anchoranalysis.math.moment: The first moment (mean) and eigenvalues of the second moments (covariance) from a matrix of points
ImageMoments(DoubleMatrix2D, boolean, boolean) - Constructor for class org.anchoranalysis.math.moment.ImageMoments: Calculates the second-moments from the covariance of a matrix of points
ImageMomentsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: A base class for features that are calculated using image-moments
ImageMomentsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
ImageSize - Class in org.anchoranalysis.plugin.io.bean.summarizer.image: Summarizes the size of images.
ImageSize() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
ImgLib2Lanczos - Class in org.anchoranalysis.image.bean.interpolator
ImgLib2Lanczos() - Constructor for class org.anchoranalysis.image.bean.interpolator.ImgLib2Lanczos
ImgLib2Linear - Class in org.anchoranalysis.image.bean.interpolator
ImgLib2Linear() - Constructor for class org.anchoranalysis.image.bean.interpolator.ImgLib2Linear
immutableAdd(Point2i, Point2i) - Static method in class org.anchoranalysis.spatial.point.Point2i: Performs an addition without changing any values in an existing point
immutableAdd(Point3d, int, int, int) - Static method in class org.anchoranalysis.spatial.point.Point3d: Performs an addition without changing any values in an existing point
immutableAdd(ReadableTuple3i, int, int, int) - Static method in class org.anchoranalysis.spatial.point.Point3i: Performs an addition without changing any values in an existing point
immutableAdd(ReadableTuple3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.Point3i: Performs an addition without changing any values in an existing point
immutableAdd(Tuple3d, Tuple3d) - Static method in class org.anchoranalysis.spatial.point.Point3d: Performs an addition without changing any values in an existing point
immutableScale(ReadableTuple3i, int) - Static method in class org.anchoranalysis.spatial.point.Point3i: Performs a scale without changing any values in an existing point
immutableScale(Tuple3d, int) - Static method in class org.anchoranalysis.spatial.point.Point3d: Performs a scale without changing any values in an existing point
immutableSubtract(ReadableTuple3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.Point3i: Performs a subtraction without changing any values in an existing point
immutableSubtract(Tuple3d, Tuple3d) - Static method in class org.anchoranalysis.spatial.point.Point3d: Performs a subtraction without changing any values in an existing point
imposeMinima(Channel, SeedCollection, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImposition
imposeMinima(Channel, SeedCollection, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
ImposeMinima - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Imposes minima in seed locations on the input-channel before performing the segmentation
ImposeMinima() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
imposeMinimumRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
ImposeResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
ImposeResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
IncludeBeanFactory - Class in org.anchoranalysis.bean.xml.factory
IncludeBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.IncludeBeanFactory
includeFirst() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
includeFirstOrSecond() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Iff true, group columns are added to the CSV exports, and other group exports may occur in sub-directories.
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects: If either a group-generator is defined or there's more than one provider, then groups should be included
IncludeListFactory<T> - Class in org.anchoranalysis.bean.xml.factory
IncludeListFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.IncludeListFactory
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
IncludeMarksFailureException - Exception in org.anchoranalysis.mpp.feature.addcriteria
IncludeMarksFailureException(Exception) - Constructor for exception org.anchoranalysis.mpp.feature.addcriteria.IncludeMarksFailureException
IncludeMarksFailureException(String) - Constructor for exception org.anchoranalysis.mpp.feature.addcriteria.IncludeMarksFailureException
includeMerged() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
includePossiblyOverlappingObject(ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
includePossiblyOverlappingObject(T, T) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
includePossiblyOverlappingObject(T, T) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy: Whether to include another (possibly-overlapping with source) element in processing?
IncludeRandomObjects - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points: 1.
IncludeRandomObjects() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
includeSecond() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
IncompleteElementRange - Interface in org.anchoranalysis.io.manifest.sequencetype: An incomplete range of discrete integers (like BoundedRangeIncomplete but with a string-representation for each index.
IncorrectImageSizeException - Exception in org.anchoranalysis.image.core.dimensions
IncorrectImageSizeException(Exception) - Constructor for exception org.anchoranalysis.image.core.dimensions.IncorrectImageSizeException
IncorrectImageSizeException(String) - Constructor for exception org.anchoranalysis.image.core.dimensions.IncorrectImageSizeException
IncorrectVoxelTypeException - Exception in org.anchoranalysis.image.voxel.datatype
IncorrectVoxelTypeException(String) - Constructor for exception org.anchoranalysis.image.voxel.datatype.IncorrectVoxelTypeException
IncorrectVoxelTypeException(Throwable) - Constructor for exception org.anchoranalysis.image.voxel.datatype.IncorrectVoxelTypeException
incr(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
incr(Reporting<S>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
incrCount(T) - Method in class org.anchoranalysis.plugin.io.summarizer.FrequencyMap
IncreaseFeatureCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
IncreaseFeatureCondition(FeatureEvaluator<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
increasingIntegers(OutputPatternIntegerSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
IncreasingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype: Indices must be integers that always increase as added.
IncreasingIntegers() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
increment() - Method in class org.anchoranalysis.math.arithmetic.Counter
increment(double) - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Adds a new item to the sum, and increments the count by 1.
increment(double, long) - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Increments both the sum and count by particular values
increment(RunningSum) - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Increments (adds) an existing RunningSum to the current.
increment(Point2d) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
increment(Point2i) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
increment(Point3d) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
increment(Point3i) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
increment(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
incrementCount(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
incrementingByOne(OutputPatternIntegerSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Writes elements to directory, with an incrementing integer in the filename.
incrementingByOneCurrentDirectory(String, String, int) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Writes elements to the current directory, with an incrementing integer in the filename.
incrementingByOneStream(OutputPatternIntegerSuffix, Stream<T>) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Writes file for each element in a stream with an incrementing integer sequence in the outputted file-name.
incrementingIntegers(OutputPatternIntegerSuffix, int, int) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
IncrementingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype
IncrementingIntegers() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
IncrementingIntegers(int) - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
IncrementingIntegers(int, int) - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
incrementSumBuffer(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer: Increments a particular offset in the sum bufffer by a certain amount
incrementValue(int) - Method in class org.anchoranalysis.math.histogram.Histogram
incrementValueBy(int, int) - Method in class org.anchoranalysis.math.histogram.Histogram
incrementValueBy(int, long) - Method in class org.anchoranalysis.math.histogram.Histogram: long version of incrValBy
incrementX() - Method in class org.anchoranalysis.spatial.point.Point2i
incrementX() - Method in class org.anchoranalysis.spatial.point.Tuple3i
incrementX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
incrementX(int) - Method in class org.anchoranalysis.spatial.point.Point2i
incrementX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
incrementY() - Method in class org.anchoranalysis.spatial.point.Point2i
incrementY() - Method in class org.anchoranalysis.spatial.point.Tuple3i
incrementY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
incrementY(int) - Method in class org.anchoranalysis.spatial.point.Point2i
incrementY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
incrementZ() - Method in class org.anchoranalysis.spatial.point.Tuple3i
incrementZ(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
incrementZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
incrEnergy(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
incrKernelAccpt(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
incrKernelProp(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
incrSize(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
incrTemperature(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
incrWorker() - Method in class org.anchoranalysis.core.progress.ProgressReporterMultiple
IndependentChannels - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Converts each channel independently and creates a single-channeled stack from the conversion.
IndependentChannels() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
index(int) - Method in class org.anchoranalysis.plugin.io.multifile.IntegerRange: Maps an original integer to it's index from (0..size]
Indexable - Class in org.anchoranalysis.core.index: Holds a single-index which is hashable and comparable.
Indexable(int) - Constructor for class org.anchoranalysis.core.index.Indexable
IndexableMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy
IndexableMarksWithEnergy(int, MarksWithEnergyBreakdown) - Constructor for class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
IndexableOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: An output-name with an index somehow appended or prepended in a particular style.
IndexableOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
IndexableOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
IndexableOutputNameStyle(IndexableOutputNameStyle) - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Copy constructor
IndexableOverlays - Class in org.anchoranalysis.overlay
IndexableOverlays(int, OverlayCollection) - Constructor for class org.anchoranalysis.overlay.IndexableOverlays
IndexBridge<T> - Class in org.anchoranalysis.core.index
IndexBridge(GetterFromIndex<T>) - Constructor for class org.anchoranalysis.core.index.IndexBridge
IndexByChannel<T> - Class in org.anchoranalysis.mpp.voxel.partition
IndexByChannel() - Constructor for class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
IndexByRegion<T> - Class in org.anchoranalysis.mpp.voxel.partition
IndexByRegion(VoxelPartitionFactory<T>, int, int) - Constructor for class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
IndexedCSVRows - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv: Stores the rows from the CSV file.
IndexedCSVRows(ReadByLine, ColumnDefinition) - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.csv.IndexedCSVRows: Creates an index of the rows of the CSV file according to a particular columnDefinition
IndexedRegionBase - Class in org.anchoranalysis.plugin.mpp.bean.region: MarkRegion with a region and an index
IndexedRegionBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
IndexGettableSettable - Interface in org.anchoranalysis.core.index
IndexGetter - Interface in org.anchoranalysis.core.index
indexIncr(String) - Method in class org.anchoranalysis.io.generator.sequence.SequenceMemory
indexInitialPoint() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
indexOf(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
indexOf(String) - Method in class org.anchoranalysis.feature.name.FeatureNameMapToIndex: The index for a particular featureName
indexOf(Mark) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
indexOf(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
IndexSetter - Interface in org.anchoranalysis.core.index
IndirectlyFromListBeanFactory<T extends AnchorBean<T>,S> - Class in org.anchoranalysis.bean.xml.factory
IndirectlyFromListBeanFactory(CheckedFunction<List<T>, S, ? extends Exception>) - Constructor for class org.anchoranalysis.bean.xml.factory.IndirectlyFromListBeanFactory
informLatestState(T) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel: Called every time a proposal is accepted, so a kernel can potentially keep track of the state of the current image
informLatestState(T) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelIndependent
init() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
init() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
init() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationCondition
init() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
init() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
init(Path) - Method in class org.anchoranalysis.io.manifest.Manifest
init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller: Should be called once before calling any other methods
init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.image.feature.bean.score.VoxelScore: Initializes the voxels-score.
init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
init(List<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
init(List<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
init(List<WithConfidence<BoundingBox>>) - Method in class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes
init(List<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy: Called before the operation begins with all proposals
init(BeanInstanceMap) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
init(Logger) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.AfterCondition
init(Logger) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
init(FeatureInitParams, Logger) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache: Initialises the cache.
init(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
init(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
init(FeatureInitParams, Feature<T>, Logger) - Method in interface org.anchoranalysis.feature.calculate.InitializableFeature
init(ArrangeStack, List<RGBStack>) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.RasterArranger
init(Mask) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
init(Mask) - Method in class org.anchoranalysis.mpp.bean.points.updatable.UpdatablePointsContainer
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3ZOnly
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
init(Generator<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
init(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
init(MPPInitParams, Logger) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ListBoundCalculator
init(VoxelPartitionFactory<T>, int, int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
init(KernelBirth<T>, KernelDeath<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace: Must be called before makeProposal
init(P, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean
init(T, Logger) - Method in interface org.anchoranalysis.bean.initializable.params.ParamsInitializer
initBeanInstance(Object, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
initBeforeCalc(KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
initBeforeCalc(KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelIndependent
initBeforeCalc(KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
InitException - Exception in org.anchoranalysis.core.exception: An exception that occurs when initializing something, and it doesn't succeed
InitException(String) - Constructor for exception org.anchoranalysis.core.exception.InitException
InitException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.InitException
InitException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.InitException
initHeaders(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
initHeaders(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
initHeaders(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
InitializableBean<B,P extends BeanInitParams> - Class in org.anchoranalysis.bean.initializable: A bean that must be initialized with some parameters before being used.
InitializableBean(PropertyInitializer, PropertyDefiner) - Constructor for class org.anchoranalysis.bean.initializable.InitializableBean
InitializableFeature<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate: A feature that should be initialized with FeatureInitParams (or a sub-class) before any calculations occur.
initializePhase(int) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Initialize the next phase of the algorithm by clearing the committed workers and jobs sets and by initializing the slack arrays to the values corresponding to the specified root worker.
initializerForMPPBeans() - Static method in class org.anchoranalysis.mpp.bean.MPPBean: Creates a property-initializes for MPP-Beans
initialKernel() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
InitParamsHelper - Class in org.anchoranalysis.image.feature.session
InitParamsWithEnergyStack - Class in org.anchoranalysis.plugin.image.task.feature
InitParamsWithEnergyStack(EnergyStack, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
InitParamsWithEnergyStack(ImageInitParams, EnergyStack) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
initRecursive(Logger) - Method in class org.anchoranalysis.bean.NullParamsBean
initRecursive(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
initRecursive(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.shared.SharedFeatureSet
initRecursive(P, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean: Inits this object, and all children objects, so long as they have P Once a Bean doesn't have P, the children are not evaluated
initRecursiveWithInitializer(PropertyInitializer<?>, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean: Initializes the bean and recursively all contained beans (who have compatible initialization requirements)
initSource(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: The value and offset for the source point (around which we process neighbors)
initSource(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: The value and offset for the source point (around which we process neighbors)
initSource(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
initSource(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
initSource(Point3i, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Specify the source-point (of which all the processed points are neighbors)
initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
initWithProposerSharedObjects(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
INPUT_IMAGE - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
INPUT_IMAGE_MASK - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
INPUT_IMAGE_VISUAL - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
InputBound<T,S> - Class in org.anchoranalysis.experiment.task: Input for executing a task, associated with shared-state and other parameters.
InputBound(T, S, Manifest, boolean, InputOutputContextStateful) - Constructor for class org.anchoranalysis.experiment.task.InputBound
InputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.io: SelectParam<Path> factory for inputs.
InputForMPPBean - Interface in org.anchoranalysis.mpp.io.input: The input can be used to initialize an MPP Bean
inputName() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
InputOutputContext - Interface in org.anchoranalysis.io.output.outputter: A context for performing input generally and outputting to a particular output-directory.
InputOutputContextStateful - Class in org.anchoranalysis.experiment.task: This exists as an implementation of InputOutputContext that exposes a StatefulMessageLogger.
InputOutputContextStateful(ExperimentExecutionArguments, Outputter, StatefulMessageLogger, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.task.InputOutputContextStateful
InputOutputContextSubdirectoryCache - Class in org.anchoranalysis.io.output.outputter: Caches a InputOutputContext for each subdirectory as they are created.
InputOutputContextSubdirectoryCache(InputOutputContext, ManifestDirectoryDescription, boolean) - Constructor for class org.anchoranalysis.io.output.outputter.InputOutputContextSubdirectoryCache
InputOutputExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.io: An experiment that uses both an InputManager to specify inputs and a OutputManager to specify outputting.
InputOutputExperiment() - Constructor for class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
InputProcessContext<S> - Class in org.anchoranalysis.plugin.image.task.feature
InputProcessContext(ExportFeatureResultsAdder, S, FeatureNameList, Optional<String>, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
inputs(ImageInitParams, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
inputs(InputManagerParams) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
inputs(InputManagerParams) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Shuffle
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
inputSelectParam(CommandLine, String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Can point to either: a path ending in .xml, assumed to BeanXML for an input manager a directory, set as an the inputDirectory in the input-context a string with a wild-card, assumed to be a glob, set into the input-context as a glob a string with a period and without any forward or backwards slashes, set into the input-context as an extension to match
inputType() - Method in class org.anchoranalysis.feature.bean.Feature: The class corresponding to feature input-type (i.e.
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureOperator
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
inputType() - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureEnergy
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureHistogram
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeaturePairObjects
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject
inputType() - Method in class org.anchoranalysis.image.feature.bean.stack.FeatureStack
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureAllMemo
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeaturePairMemo
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureMark
inputType() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
inputType() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
inputType() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
inputTypesExpected() - Method in class org.anchoranalysis.experiment.bean.task.HelloWorld
inputTypesExpected() - Method in class org.anchoranalysis.experiment.bean.task.Task: Highest class(es) that will function as a valid input.
inputTypesExpected() - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
inputTypesExpected() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
inputTypesExpected() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Highest class(es) that will function as a valid input.
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
InputTypesExpected - Class in org.anchoranalysis.experiment.task: A list of base (parent) classes for input-types that a task expects
InputTypesExpected(Class<? extends InputFromManager>) - Constructor for class org.anchoranalysis.experiment.task.InputTypesExpected
insertAfter(List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath: Inserts points at end of existing path.
insertBefore(List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath: Inserts points before existing path.
insertBeginning(String) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Inserts a new feature-name at the beginning of the list
insertBeginning(String[]) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Inserts new feature-names at the beginning of the list
InsertRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive: Generates an out string where $digit$ is replaced with the #digit group from a regex
InsertRegExGroups() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
InsertRegExGroups(RegEx, String) - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
InsideBoxOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions: Creates a binary img-channel where all pixels are 'on' within a certain x, y, z coordinate range
InsideBoxOn() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
inSlices - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
instance - Static variable in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
instance() - Static method in class org.anchoranalysis.bean.initializable.params.NullInitParams
instance() - Static method in class org.anchoranalysis.feature.input.FeatureInputNull
instance() - Static method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
instance() - Static method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory: Singleton
instance() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: Singleton
instance() - Static method in class org.anchoranalysis.io.bioformats.ConfigureBioformatsLogging
instance() - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMapSingleton
instance() - Static method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
instance() - Static method in class org.anchoranalysis.plugin.io.input.path.RootPathMap
INSTANCE - Static variable in class org.anchoranalysis.experiment.task.NoSharedState
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.All: A singleton instance of All.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix: A singleton instance of IgnoreUnderscorePrefix.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.None: A singleton instance of None.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.rules.Permissive: A singleton instance of Permissive.
InsufficientPointsException - Exception in org.anchoranalysis.mpp.bean.points.fitter
InsufficientPointsException() - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
InsufficientPointsException(String) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
InsufficientPointsException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
InsufficientPointsException(Throwable) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
IntBinaryOperation - Interface in org.anchoranalysis.core.functional.checked: A binary operation on two int-values that produces an int
IntegerRange - Class in org.anchoranalysis.plugin.io.multifile
IntegerRange(int) - Constructor for class org.anchoranalysis.plugin.io.multifile.IntegerRange
IntegerRange(int, int) - Constructor for class org.anchoranalysis.plugin.io.multifile.IntegerRange
IntegerSequenceContaner - Class in org.anchoranalysis.core.index.bounded
IntegerSequenceContaner(int) - Constructor for class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
integerSet() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
IntegerSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle: Outputs a file-name involving an integer of length numberDigits with leading zeros.
IntegerSuffixOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
IntegerSuffixOutputNameStyle(String, int) - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
IntegerSuffixOutputNameStyle(String, String, int) - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Calculates a statistic from the intensity values covered by a single object-mask in a channel.
Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity: The intensity of a particular channel of the stack, by default the mean-intensity.
Intensity - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
Intensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
Intensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
Intensity() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
IntensityGradientBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
IntensityGradientBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
IntensityGreaterEqualThan - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only keep objects where at least one voxel (on a particular channel) has intensity greater or equal to a threshold.
IntensityGreaterEqualThan() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
intensityMax(Voxels<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Finds the maximum intensity-value (as an int) among all voxels.
IntensityMeanCalculator - Class in org.anchoranalysis.plugin.image.intensity
IntensityMeanMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
IntensityMeanMaxSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
IntensityMeanShell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
IntensityMeanShell() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShell
IntensityMeanShellBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Constructs a shell around an object-mask using a standard dilation and erosion process
IntensityMeanShellBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
IntensityMeanShellMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
IntensityMeanShellMaxSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellMaxSlice
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in interface org.anchoranalysis.image.voxel.interpolator.Interpolator: Interpolates from voxelsSource to voxelsDestination for unsigned 8-bit buffers.
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in interface org.anchoranalysis.image.voxel.interpolator.Interpolator: Interpolates from voxelsSource to voxelsDestination for unsigned 16-bit buffers.
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
InterpolateUtilities - Class in org.anchoranalysis.image.voxel.interpolator
Interpolator - Interface in org.anchoranalysis.image.voxel.interpolator
InterpolatorBean - Class in org.anchoranalysis.image.bean.interpolator
InterpolatorBean() - Constructor for class org.anchoranalysis.image.bean.interpolator.InterpolatorBean
InterpolatorBeanImageJ - Class in org.anchoranalysis.plugin.imagej.bean.interpolator
InterpolatorBeanImageJ() - Constructor for class org.anchoranalysis.plugin.imagej.bean.interpolator.InterpolatorBeanImageJ
InterpolatorFactory - Class in org.anchoranalysis.image.voxel.interpolator
InterpolatorImgLib2 - Class in org.anchoranalysis.image.voxel.interpolator: Performs interpolation using ImgLib2
InterpolatorImgLib2(InterpolatorFactory<UnsignedByteType, RandomAccessible<UnsignedByteType>>, InterpolatorFactory<UnsignedShortType, RandomAccessible<UnsignedShortType>>) - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2
InterpolatorImgLib2Lanczos - Class in org.anchoranalysis.image.voxel.interpolator
InterpolatorImgLib2Lanczos() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Lanczos
InterpolatorImgLib2Linear - Class in org.anchoranalysis.image.voxel.interpolator
InterpolatorImgLib2Linear() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Linear
InterpolatorImgLib2NearestNeighbor - Class in org.anchoranalysis.image.voxel.interpolator
InterpolatorImgLib2NearestNeighbor() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2NearestNeighbor
InterpolatorNone - Class in org.anchoranalysis.image.voxel.interpolator: Doesn't do any interpolation, just copies values
InterpolatorNone() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
intersect(ObjectMask, Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Intersects this object-mask with another
IntersectingCircleObjectsFixture - Class in org.anchoranalysis.test.feature.plugins.objects
intersection() - Method in class org.anchoranalysis.spatial.box.BoundingBox: For evaluating the intersection between this bounding-box and others
Intersection - Class in org.anchoranalysis.plugin.image.bean.object.match
Intersection - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair: Finds the intersection of two objects and calculates a feature on it
Intersection() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Intersection
Intersection() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
IntersectionOverUnion - Class in org.anchoranalysis.plugin.image.box: Calculates the intersection-over-union score a pair of bounding-boxes.
intersectsWith(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree: All objects that intersect with another object.
intersectsWith(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
intersectsWith(BoundingBox) - Method in class org.anchoranalysis.spatial.rtree.RTree
IntersectsWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Keeps objects which intersects with ANY ONE of a collection of other objects.
IntersectsWith() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
intersectsWithAsIndices(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
IntersectsWithContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Returns only the objects that intersect with at least one object in the container
IntersectsWithContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
intersectWith(Extent) - Method in class org.anchoranalysis.spatial.Extent: Intersects this extent with another (i.e.
intFromDoubleCeil(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
intFromDoubleFloor(Point2d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
intFromDoubleFloor(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
intFromFloat(Point3f, boolean) - Static method in class org.anchoranalysis.spatial.point.PointConverter
INVALID_AXIS_INDEX - Static variable in class org.anchoranalysis.spatial.axis.AxisTypeConverter
INVALID_AXIS_STRING - Static variable in class org.anchoranalysis.spatial.axis.AxisTypeConverter
invalidate() - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache: Invalidates existing caches so all calculations occur freshly
invalidate() - Method in interface org.anchoranalysis.feature.calculate.cache.ResettableCalculation: Resets the cached-calculation, so the next call to doOperationWithParams() is guaranteed to calculation the operation, and store the value in the cache.
invalidate() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
invalidate() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap: Invalidates the cache, removing any items already stored.
invalidate() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
invalidate() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
invalidateExcept(Set<ChildCacheName>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache: Invalidates existing caches so all calculations occur freshly - except some particular child-caches who are not invalidated
invalidateExcept(Set<ChildCacheName>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
invalidateExcept(Set<ChildCacheName>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
InvalidPathArgumentException - Exception in org.anchoranalysis.launcher.executor.selectparam.path: An exception throw if an invalid-path is inputted as an argument.
InvalidPathArgumentException(String, InvalidPathException) - Constructor for exception org.anchoranalysis.launcher.executor.selectparam.path.InvalidPathArgumentException
invert() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Changes the OFF state to be the ON state and vice-versa.
invert() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
invert() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Produces a new object-mask that uses the same voxel-buffer but inverts the OFF and ON
invert() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
invert(Mask) - Static method in class org.anchoranalysis.image.core.mask.MaskInverter: Modifies a mask so that OFF voxels become ON voxels and vice versa
Invert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Subtracts each voxel from the maximum value for the channel's data type (e.g.
Invert - Class in org.anchoranalysis.plugin.image.bean.mask.provider: Switches on voxels to off and vice-versa.
Invert - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Performs a segmentation and inverts and ON and OFF bytes
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.Invert
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Invert
InvertedMax<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic: Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.
InvertedMax() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
invertObjectDuplicate(ObjectMask) - Static method in class org.anchoranalysis.image.core.mask.MaskInverter: Creates a new object-mask where OFF voxels become ON voxels and vice versa
isAccepted() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
isAccepted() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
isAccepted() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
isAcceptNoResolution() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
isAcceptOutsideScene() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
isAddName() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
isAddOne() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
isApplyResolution() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: Multiples the values by the x-resolution, if it exists.
isAsPercentage() - Method in class org.anchoranalysis.feature.bean.results.Quantile: If true, the quantile is interpreted as a percentage rather than a decimal
isAtLeastOnePositive() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Checks that at least one of iterationsDilation and iterationsErosion is more than 0
isAvoidBulletOnFirst() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate: Iff true no bullet is added for the very first-item in the list
isAvoidDivideByZero() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
isAvoidOverlappingObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: If true, no overlapping objects are treated as pairs
isBest() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
isBest() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
isBigNeighborhood() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters: iff true uses a big-neighborhood (8 or 26 connectivity) for dilation
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask: If true uses 8 neighborhood rather than 4 neighborhood etc.
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents: if true, uses 8 neighborhood instead of 4, and similarly in 3d
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
isBit0() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
isBit1() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
isBit2() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
isBit3() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
isBit4() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
isBit5() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
isBit6() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
isBit7() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderXY
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderZ
isBySlices() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
isCalledRegisterAllPackage() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
isCellUsed(int, int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
isChangeExisting() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase: If true, the existing channel can be changed.
isClearOutsideMask() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
isClosed() - Method in class org.anchoranalysis.spatial.Contour
isCollapseFilename() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
isCompatibleWith(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Can these parameters be used with a particular feature?
isCompatibleWith(Mark) - Method in interface org.anchoranalysis.mpp.mark.CompatibleWithMark
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.EllipseBoundsCheck
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceAbstractPosition
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceRadii
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.CreateNew
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.UniformRandom
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomXY
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelReplacePartition
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ConstantWeight
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.NumberPoints
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
isCompleted() - Method in class org.anchoranalysis.experiment.task.processor.JobState
isCompletedFailure() - Method in class org.anchoranalysis.experiment.task.processor.JobState
isCompletedSuccessfully() - Method in class org.anchoranalysis.experiment.task.processor.JobState
isConditionTrue() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
isConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
isConnectedComponentIDCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
isConnectedComponentIDCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
isConsiderForMerge() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
isConvexHull() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects: If true, Reduces the set of points by applying a convex-hull operation
isCov() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
isCreateShort() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
isCreateShort() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
isCreateShort() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
isCreateShort() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew: If True creates an unsigned short-image
isCsvIgnoreZeros() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: Iff true, bins with zero-counts are not written as a row in the CSV file.
isDatasetNameSubdirectory() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: If true the datasetName is appended as a subdirectory e.g.
isDay() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If true, the current day (yyyy.MM.dd) is included in the output
isDebug() - Method in class org.anchoranalysis.bean.shared.path.RootPath: If true this root is preferred, when executing a job in debugging mode
isDebug() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
isDebugEnabled() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
isDebugEnabled() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Is debug-mode enabled?
isDebugEnabled() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
isDebugMode() - Method in class org.anchoranalysis.io.output.path.prefixer.FilePathPrefixerContext
isDebugModeEnabled() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
isDefault() - Method in class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
isDefault() - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam: Is this the default option that occurs without any additional user effort?
isDefault() - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
isDetailedLogging() - Method in class org.anchoranalysis.experiment.task.InputBound
isDetailedLogging() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment: Iff true, additional log messages are written to describe each job in terms of its unique name, output folder, average execution time etc.
isDifferentColorsForMatches() - Method in class org.anchoranalysis.annotation.io.assignment.generator.ColorPool
isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Is this buffer direct or non-direct?
isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Is this buffer direct or non-direct?
isDirectionChainCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
isDirectionChainCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
isDisableDebugMode() - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
isDisableDebugMode() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
isDisablePathModification() - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
isDo3D() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
isDo3D() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Whether to perform the morphological dimensions in 3D or 2D
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
isDo3D() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
isDummyMode() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
isDuplicate() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: If true the channel is duplicated after it is retrieved, to prevent overwriting existing data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
isDuplicate() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
isEmpty() - Method in interface org.anchoranalysis.bean.StringBeanCollection
isEmpty() - Method in class org.anchoranalysis.bean.StringList
isEmpty() - Method in class org.anchoranalysis.bean.StringSet
isEmpty() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider: Are there any items in the provider
isEmpty() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
isEmpty() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
isEmpty() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
isEmpty() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
isEmpty() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
isEmpty() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: If no output-names exist.
isEmpty() - Method in class org.anchoranalysis.math.histogram.Histogram
isEmpty() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
isEmpty() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
isEmpty() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
isEmpty() - Method in class org.anchoranalysis.spatial.box.PointRange: Has a valid min and max defined? In other words, has at least one point been added?
isEmpty() - Method in class org.anchoranalysis.spatial.Extent
isEnabled() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
isErodeAtBoundary() - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
isErrorDisconnectedObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels: If true, throws an error if there is a disconnected object after the erosion
isEvaluated() - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
isExceptionIfEmpty() - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic: If true, then an exception is thrown if the histogram is empty, otherwise is returned.
isExcludeZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Iff true, zero-valued voxels are excluded from the histogram
isExcludeZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
isExcludeZero() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity: If true, zeros are excluded from considering in the histogram
isExecuting() - Method in class org.anchoranalysis.experiment.task.processor.JobState
isExitBeforeOptimization() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Iff true the algorithm exits before optimization begins (useful for debugging).
isExitWithMinima() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong: If true, exits early and just returns the minima, without any further segmentation
isExtendInZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages: Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all slices)
isFindMaxima() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice: If true, the maxima of the score is searched for.
isFinished() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
isFirst() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle: Iff true, first object is used, otherwise the second
isFirstLineHeaders() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
isFixRandomSeed() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Iff true uses a constant seed for the random-number-generator (useful for debugging).
isFlatten() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline: If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D
isFlatten() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced
isForceBinary() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
isForceChangeBytes() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.
isForceDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Whether more detailed log-messages around each experiment occur.
isForceEagerEvaluation() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
isForceRGB() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster: If set, ensures every stack is converted into 3 channels
isForwardDirectionOnly() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
isGaussian() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: If true, the Gaussian filter is included
isGPU() - Method in class org.anchoranalysis.core.concurrency.WithPriority
isHighestTwoRadiiOnly() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
isIgnoreAtThreshold() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
isIgnoreAtThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
isIgnoreCase() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
isIgnoreFileNotFoundAppend() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
isIgnoreFittingFailure() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects: If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply not included (with only a log error) If false, an exception is thrown
isIgnoreHidden() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
isIgnoreHigherSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
isIgnoreLowerSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
isIgnoreMissingChannel() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels: Iff true and we cannot find a channel in the file, we ignore it and carry on
isIgnoreNaN() - Method in class org.anchoranalysis.feature.bean.operator.Sum: If true, we ignore any NaN values.
isIgnoreNoObjects() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: If true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.
isIgnoreRangeAxisOutside() - Method in class org.anchoranalysis.plot.index.LinePlot
isIgnoreZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
isIncludeFeatureNames() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features
isIncludeFileName() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
isIncludeFirst() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the First-object of the pair
isIncludeFolders() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure: If false, the folders are ignored, and only the file-name is used in the output
isIncludeMerged() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Merged-object of the pair
isIncludeSecond() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Second-object of the pair
isIncludeShell() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
isIncludeZ() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
isInitialized() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor: Is an input-object compatible with this particular task?
isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.bean.task.Task: Is an input-object compatible with this particular task?
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
isInterpolate() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
isInverse() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
isInverse() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is removed)
isInverseMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
isInvert() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
isInvert() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
isInvert() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch: Iff true, then a file is rejected if regEx matches and vice-versa (opposite to normal behaviour)
isInvertDecisionValue() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
isItemIncluded(T) - Method in class org.anchoranalysis.plot.bean.Plot: Whether to include this particular item in the plot?
isKeepEntireImage() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages: If true, rather than writing out a bounding-box around the object-mask, the entire image is written
isKeepExtremes() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
isKeepZ() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Keep the z-resolution if it is already defined
isKeyRequired() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
isLabel() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: If true a label is added beside every image showing the slice index
isLeaf() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
isLogPath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the pathIn and pathOut are logged.
isMarksSpan() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
isMarksSpan(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
isMarksSpan(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
isMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
isMedian() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: If true, the median filter is included
isMemberFlag(byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr
isMemberFlagAnd(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
isMemberFlagOr(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
isMerge() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
isMinima(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
isMinima(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
isMip() - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
isMip() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
isMip() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhood
isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodIgnoreOutsideScene
isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask
isNewValuesPossible() - Method in interface org.anchoranalysis.image.voxel.interpolator.Interpolator: Returns true if it's possible for values to be created after interpolation that aren't found in the input-image.
isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Lanczos
isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Linear
isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2NearestNeighbor
isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
isNoBlack() - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
isNormalize() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
isNormalize() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
isNormalizeFeatures() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier: Normalize features
isNoScale() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor: If the scale-factor involves no scaling at all
isNumeric() - Method in class org.anchoranalysis.core.value.TypedValue
isNumeric() - Method in class org.anchoranalysis.io.output.bean.ReportFeature
isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
isNumeric() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
isNumeric() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
isNumeric() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
isOff(byte) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
isOff(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
isOff(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
isOn() - Method in interface org.anchoranalysis.io.generator.sequence.OutputSequence
isOn() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing
isOn() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed
isOn(byte) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
isOn(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
isOn(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
isOutline() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, an outline is drawn around the entries.
isOutlineAtBoundary() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
isOutputCSV() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize: Iff true, a mapping.csv file is created showing the mapping between the original-names and the anonymized versions
isOutputEnabled() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.All
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.None
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelInSet
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelNot
isOutputEnabled(String) - Method in interface org.anchoranalysis.io.output.enabled.single.SingleLevelOutputEnabled: Is a particular a particular output-enabled?
isOutputShort() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: Iff true, outputs a short channel, otherwise byte channel
isOutsideAtThreshold() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
isOutsideAtThreshold() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
isOutsideAtThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
isOutsideAtThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
isParamPrefixAppendNumber() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder: If true the constant is appended to the param prefix (a dot and a number)
isPhysical() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
isPlateau(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Is the payload considered in making decisions? (iff false, payload of nodes is irrelvant)
isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>, boolean) - Static method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
isPointInside(DrawOverlay, Point3i) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
isPointInside(DrawOverlay, Point3i) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
isPointInside(DrawOverlay, Point3i) - Method in class org.anchoranalysis.overlay.Overlay: Is a point inside an overlay? (for a particular OverlayWriter).
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.Mark
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.PointList
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
isPointOn(Point3i) - Method in class org.anchoranalysis.image.core.mask.Mask
isPointOnMask(Point3d, EnergyStack, Function<Point3d, Point3i>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
isPrefix() - Method in class org.anchoranalysis.bean.define.adder.FromXmlList: If true, a prefix is prepended to the name of each added bean.
isPreserveExtensionIfDuplicate() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions: Keeps the extension if the file-name (without the extension) becomes duplicated with another
isPreventObjectIntersection() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters: Iff true, objects can only be neighbors if they have no intersecting voxels.
isProposal() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
isProposed() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
isRadiusInMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
isRecordedAsEnabled(String) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Is a particular output-name recorded as enabled?
isRecurseSubfolders() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
isRecursive() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: Whether to apply the search recursively or not
isRejectIterationIfAllLow() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
isRejectIterationIfDisconnected() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.EqualTo
isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.GreaterThan
isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.GreaterThanEqualTo
isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.LessThan
isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.LessThanEqualTo
isRelationToValueTrue(double, double) - Method in interface org.anchoranalysis.math.relation.RelationToValue
isRemoveExtensionInDescription() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories: Whether to remove the file-extension from the filename.
isRemoveTouchingBorderXY() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
isReplaceMatchesWithSolids() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
isReplaceWithMidpoint() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
isReportFitterErrors() - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
isRequireAllFilesMatch() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
isRequireBBoxNeighbors() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch
isRequireTouching() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires the object-masks to touch.
isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceInfinity
isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceNaN
isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
isRewardHigherSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore: Treat the higher side as if it's the the fill cdf
isRewardLowerSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
isRgb() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: If true, the output contains three channels (the input and two duplicates) instead of one
isRGB() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
isRGB() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
isRGB() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions: Is it an image with three channels (red, green and blue)?
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
isRootInStructure() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: If true the directory structure is ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
isRotateOnlyIn2DPlane() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
isSecond() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: Only relevant if time==true.
isSecondary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter: If proposal is true, this toggles between the primary and secondary proposal
isSelective() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern: Whether the output should be checked to see if it is allowed or not.
isShowAgg() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
isShowBest() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
isShowDomainAxis() - Method in class org.anchoranalysis.plot.index.BarPlot
isShowVerticalAxisLines() - Method in class org.anchoranalysis.plot.PlotInstance
isSigmaInMeters() - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
isSilentlyDeleteExisting() - Method in class org.anchoranalysis.io.output.bean.OutputManager: Whether to silently first delete any existing output at the intended path, or rather throw an error.
isSilentlyDeleteExisting() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
isSkipAtBorder() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles: If true we do not fill any objects that touch the border
isSkipFileName() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories: Iff true the filename is not considered, only the subdirectories.
isSkipFileName() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
isSkipMissingChannels() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
isSlicesSeparately() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
isStackAsChannel() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick: If true, a raster-stack is treated as a single-channel, even if multiple exist (and no additionalChannel is set)
isStackBackground() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
isStrongEdgeEnhancer() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: Enables the StrongEdgeEnhancer diffusion function
isSubtractFromMaskOnly() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
isSuppress3D() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
isSuppress3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
isSuppress3D() - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
isSuppressErrors() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
isSuppressExceptions() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
isSuppressExceptions() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
isSuppressExceptions() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
isSuppressExceptions() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
isSuppressOutlineZ() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: if true, the outline is suppressed in the z-dimension i.e.
isSuppressRes() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
isSuppressRootOut() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML.
isSuppressSeries() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: If true, the series index is not included in the outputted file-names.
isSuppressSubfolders() - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
isSuppressZ() - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
isSuppressZ() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
isSuppressZ() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: If true co-voariance is suprpessed in z-dimension
isSuppressZ() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
isSuppressZ() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
isSuppressZ() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
isSuppressZ() - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase: Iff true, surpresses covariance in the z-direction.
isSuppressZCovariance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
isSuppressZCovariance() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
isTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
isTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
isTestBothDirections() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters: iff true each combination of neighbors is tested only once, otherwise twice
isThrowExceptionForInsufficientPoints() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
isThumbnailsEnabled() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
isTime() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If true, the current time (HH.mm.ss) is included in the output
isTransposed() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
isUnbounded() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
isUnboundedAtBothEnds() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
isUnboundedOrOutsideRange(double) - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
isUnboundedOrOutsideRangeAtBothEnds(double) - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
isUniformlySized() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
isUniformTyped() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
isUnstarted() - Method in class org.anchoranalysis.experiment.task.processor.JobState
isUnvisited(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
isUnvisited(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
isUseLastSeriesIndexOnly() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
isUseLastSeriesIndexOnly() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
isUseMax() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
isUseMax() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
isUseMIP() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
isUseMIP() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
isUseZ() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
isUseZ() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
isUseZ() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
isVaryColors() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: If true the colors change for different objects in the image (using a default color set).
isZOnly() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
iterateBins(Histogram.BinConsumer) - Method in class org.anchoranalysis.math.histogram.Histogram: Calls consumer for every bin-value, increasing from min to max.
iterateBinsUntil(int, Histogram.BinConsumer) - Method in class org.anchoranalysis.math.histogram.Histogram: Calls consumer for every bin-value until a limit, increasing from min to limit (inclusive).
iterateMap(Map<K, V>, CheckedBiConsumer<K, V, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Iterate through all entries in a Map.
iterateOverSlices(Consumer<VoxelBuffer<T>>) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex: Calls sliceConsumer once for each slice with the respective buffer
iterateOverSlicesAndOffsets(ProcessVoxelBufferUnary<T>) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex: Calls process for each offset in each slice
iterateOverXY(OffsettedScalarTwoDimensionalConsumer<E>) - Method in class org.anchoranalysis.spatial.Extent: Calls processor once for each x and y-values in the range.
iterateOverXY(PointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.Extent: Calls processor once for each x and y-values in the range.
iterateOverXYOffset(CheckedIntConsumer<E>) - Method in class org.anchoranalysis.spatial.Extent: Calls processor once for each x and y-values but only passing an offset.
iterateOverXYOffset(OffsettedPointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.Extent: Calls processor once for each x and y-values in the range.
iterateOverXYWithShift(Point2i, PointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.Extent: Calls processor once for each x and y-values in the range, with a shift added.
iterateOverZ(CheckedIntConsumer<E>) - Method in class org.anchoranalysis.spatial.Extent: Calls processor once for each z-value in the range
iterateOverZUntil(IntPredicate) - Method in class org.anchoranalysis.spatial.Extent: Calls processor once for each z-value in the range unless indexPredicate returns false.
IterateVoxelsAll - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over all voxels in one or more Voxels.
IterateVoxelsBoundingBox - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of image voxels within a bounding-box.
IterateVoxelsEqualTo - Class in org.anchoranalysis.image.voxel.iterator: Like IterateVoxelsAll but specifically for equal-to operations on Voxels of type UnsignedByteBuffer.
IterateVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like IterateVoxelsBoundingBox but specifically for processing areas of intersection between BoundedVoxels of type UnsignedByteBuffer.
IterateVoxelsMask - Class in org.anchoranalysis.image.core.mask: Utilities for iterating over the subset of voxels corresponding to an on state in a Mask.
IterateVoxelsNeighbors - Class in org.anchoranalysis.image.voxel.iterator.neighbor: Utilities for iterating over the neighboring voxels to a given point.
IterateVoxelsObjectMask - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of voxels corresponding to an on state in an ObjectMask.
IterateVoxelsObjectMaskOptional - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of voxels corresponding to an on state in an optional ObjectMask.
IterateVoxelsRemaining - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over remaining voxels in one or more VoxelBuffers.
iterator() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: An iterator for each element in the sequence
iterator() - Method in class org.anchoranalysis.bean.StringList
iterator() - Method in class org.anchoranalysis.bean.StringSet
iterator() - Method in class org.anchoranalysis.core.color.ColorList
iterator() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
iterator() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
iterator() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
iterator() - Method in class org.anchoranalysis.feature.io.name.CombinedName
iterator() - Method in class org.anchoranalysis.feature.io.name.SimpleName
iterator() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
iterator() - Method in class org.anchoranalysis.feature.name.FeatureNameList
iterator() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
iterator() - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
iterator() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
iterator() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
iterator() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
iterator() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
iterator() - Method in class org.anchoranalysis.image.core.stack.Stack
iterator() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
iterator() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
iterator() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
iterator() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
iterator() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
iterator() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
iterator() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
iterator() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
iterator() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
iterator() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
iterator() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
iterator() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
iterator() - Method in class org.anchoranalysis.overlay.OverlayProperties
iterator() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
iterator() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
iterator() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
iterator() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
iteratorCoupledManifests() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
iteratorCoupledManifestsFor(Manifest) - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
iteratorExperimentalManifests() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition

J

JobDescription - Class in org.anchoranalysis.experiment.task.processor
JobDescription(String, int) - Constructor for class org.anchoranalysis.experiment.task.processor.JobDescription
jobDirectory() - Static method in class org.anchoranalysis.io.manifest.finder.match.DirectoryMatch
JobExecutionException - Exception in org.anchoranalysis.experiment: An exception that occurs when a job is executed.
JobExecutionException(String) - Constructor for exception org.anchoranalysis.experiment.JobExecutionException
JobExecutionException(String, Throwable) - Constructor for exception org.anchoranalysis.experiment.JobExecutionException: A string message displayed to the user as well as a stack-trace of the cause
JobExecutionException(Throwable) - Constructor for exception org.anchoranalysis.experiment.JobExecutionException
JobProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor: Processes a job
JobProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.JobProcessor
JobRootDirectory - Class in org.anchoranalysis.io.manifest.directory: The root directory for where outputs for a particular experiment occur.
JobRootDirectory() - Constructor for class org.anchoranalysis.io.manifest.directory.JobRootDirectory
JobStartStopLogger - Class in org.anchoranalysis.experiment.task.processor: Logs events when jobs start and stop, with or without errors.
JobStartStopLogger(String, ConcurrentJobMonitor, boolean, int, Optional<MessageLogger>) - Constructor for class org.anchoranalysis.experiment.task.processor.JobStartStopLogger: Creates a job-logger.
JobState - Class in org.anchoranalysis.experiment.task.processor
JobState() - Constructor for class org.anchoranalysis.experiment.task.processor.JobState
JoinRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive: Generates an outstring of the form
JoinRegExGroups() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups

K

Kernel - Class in org.anchoranalysis.image.voxel.kernel
Kernel<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel: Modifies an Object by applying a kernel
Kernel() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
Kernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.Kernel
kernelAccepted(Kernel<S>, Optional<T>, T, TransformationContext) - Method in interface org.anchoranalysis.plugin.mpp.segment.kernel.updater.KernelUpdater: Informs that a proposal from a particular kernel has been accepted
kernelAccepted(Kernel<S>, Optional<T>, T, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.kernel.updater.KernelUpdaterSimple
kernelAssigner() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
KernelAssigner<S,T> - Interface in org.anchoranalysis.mpp.segment.kernel
KernelAssignerAddErrorLevel<S,T> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.assigner
KernelAssignerAddErrorLevel(KernelAssigner<S, T>, ErrorNode) - Constructor for class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerAddErrorLevel
KernelAssignerCalculateEnergyFromKernel<S,T> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.assigner
KernelAssignerCalculateEnergyFromKernel(KernelStateBridge<S, T>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerCalculateEnergyFromKernel
KernelBirth<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent: Adds a new mark (a "birth") to create a proposal
KernelBirth() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
KernelBirthAndKill - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelBirthAndKill() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
KernelBirthPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark: Proposes new marks ONLY if they haven't already been proposed and accepted.
KernelBirthPartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
KernelBirthPixelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized: As an example, this is like sampling WITH replacement.
KernelBirthPixelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
KernelBirthPixelized(MarkProposer) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
KernelCalculateEnergyException - Exception in org.anchoranalysis.mpp.segment.kernel
KernelCalculateEnergyException(String) - Constructor for exception org.anchoranalysis.mpp.segment.kernel.KernelCalculateEnergyException
KernelCalculateEnergyException(String, Exception) - Constructor for exception org.anchoranalysis.mpp.segment.kernel.KernelCalculateEnergyException
KernelCalculationContext - Class in org.anchoranalysis.mpp.segment.kernel
KernelCalculationContext(MarkFactoryContext, EnergyStack, EnergySchemeWithSharedFeatures, RandomNumberGenerator, ErrorNode) - Constructor for class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
KernelDeath<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelDeath() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
KernelDeath.MarkAnd<S,T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelDeathPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
KernelDeathPartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelDeathPartition
KernelDeathPixelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized
KernelDeathPixelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelDeathPixelized
KernelDependent<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel
KernelDependent() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.KernelDependent
KernelDescision - Class in org.anchoranalysis.mpp.segment.kernel.proposer: A description of the decision made to accept/reject a kernel at a particular time instance (index)
KernelDescision(KernelWithIdentifier<?>, boolean, boolean, int[], long, int, ProposerFailureDescription) - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
kernelDescription() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
KernelExchange - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelExchange() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
kernelIdentifier() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
KernelIndependent<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel: A kernel that makes proposals independently of the current state
KernelIndependent() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.KernelIndependent
KernelInitialMarksFromPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelInitialMarksFromPartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
KernelInitialMarksProposed - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelInitialMarksProposed() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
KernelInitialMarksVoxelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelInitialMarksVoxelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
KernelInitialMarksVoxelized(MarkCollectionProposer) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
KernelIterDescriptionSerializerPeriodicReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
KernelIterDescriptionSerializerPeriodicReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.KernelIterDescriptionSerializerPeriodicReporter
KernelMerge - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelMerge() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
KernelPosNeg<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel
KernelPosNeg() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
KernelProposer<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel.proposer
KernelProposer() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
KernelProposerOption<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel.proposer
KernelProposerOption() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
KernelProposerOptionDual<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
KernelProposerOptionDual() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
KernelProposerOptionSingle<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
KernelProposerOptionSingle() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
KernelProposerOptionSingle(Kernel<T>, double) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
KernelReplace<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelReplace() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
KernelReplacePartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
KernelReplacePartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelReplacePartition
KernelSplit - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
KernelSplit() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
kernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
kernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
kernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
KernelStateBridge<U,T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge: Transforms a kernel-to-state and vice versa
KernelStateBridge() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridge
KernelStateBridgeIdentity<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge: No transformation occurs as Kernel and State are the same type
KernelStateBridgeIdentity() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeIdentity
KernelStateBridgePixelize<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge: State derived from the kernel takes the form of ToPixelized<T>
KernelStateBridgePixelize() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
KernelStateBridgeTransformer<U,T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
KernelStateBridgeTransformer() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridge
kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeIdentity
kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
KernelUpdater<S,T> - Interface in org.anchoranalysis.plugin.mpp.segment.kernel.updater
KernelUpdaterSimple<S,T> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.updater
KernelUpdaterSimple(ListUpdatableMarkSetCollection, WeightedKernelList<S>, StateTransformer<Optional<T>, Optional<S>>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.kernel.updater.KernelUpdaterSimple
KernelWithIdentifier<T> - Class in org.anchoranalysis.mpp.segment.kernel.proposer
KernelWithIdentifier(Kernel<T>, int) - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
keys() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider: Returns a set of keys associated with the provider.
keys() - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
keys() - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
keys() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
keys() - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
keys() - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
keys() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
keys() - Method in class org.anchoranalysis.image.core.stack.NamedStacks
keys() - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequence
keys() - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
keys() - Method in class org.anchoranalysis.image.core.stack.wrap.WrapTimeSequenceAsStack
keySet() - Method in class org.anchoranalysis.core.value.KeyValueParams
keySet() - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
keysEvaluated() - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
KeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.params: A key and associated value
KeyValueCondition() - Constructor for class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
keyValueParams() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
KeyValueParams - Class in org.anchoranalysis.core.value: Parameters represented by key/value strings
KeyValueParams() - Constructor for class org.anchoranalysis.core.value.KeyValueParams
KeyValueParamsDeserializer<T> - Class in org.anchoranalysis.core.serialize
KeyValueParamsDeserializer() - Constructor for class org.anchoranalysis.core.serialize.KeyValueParamsDeserializer
KeyValueParamsForImageCreator - Class in org.anchoranalysis.mpp.feature.energy.scheme: Creates KeyValueParams for a particular EnergyStack that is associated with a EnergyScheme
KeyValueParamsForImageCreator(EnergyScheme, SharedFeatureMulti, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.KeyValueParamsForImageCreator
KeyValueParamsGenerator - Class in org.anchoranalysis.io.generator.serialized
KeyValueParamsGenerator(String) - Constructor for class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
KeyValueParamsInitParams - Class in org.anchoranalysis.bean.shared.params.keyvalue
KeyValueParamsProvider - Class in org.anchoranalysis.bean.shared.params.keyvalue
KeyValueParamsProvider() - Constructor for class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProvider
KeyValueParamsProviderReference - Class in org.anchoranalysis.bean.shared.params.keyvalue
KeyValueParamsProviderReference() - Constructor for class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
kurtosis(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics
Kurtosis - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Kurtosis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Kurtosis

L

l2norm() - Method in class org.anchoranalysis.spatial.point.Point3d
labelElements(Channel, List<T>, Optional<Map<Integer, T>>) - Method in class org.anchoranalysis.image.core.object.label.LabelObjects: Replaces the contents of the channel so that all element's voxels are labelled with successive unique integer identifiers 1,2,3 etc.
labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
labelFor(ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Determines a particular group-identifier for an input
labelFor(ImageCSVLabellerInitParams, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
labelFor(ImageLabellerStringMapInitParams<T>, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
labelFor(T, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller: Determines a particular group-identifier for an input
labelForAggregation() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: A label to be used when aggregrating this annotation with others, or null if this makes no sense
LabelHeaders - Class in org.anchoranalysis.feature.io.results: Headers in a CSV file for the non-results (i.e.
LabelHeaders(String[]) - Constructor for class org.anchoranalysis.feature.io.results.LabelHeaders: Creates with only non-group headers
LabelHeaders(String[], String[]) - Constructor for class org.anchoranalysis.feature.io.results.LabelHeaders
LabelObjects<T> - Class in org.anchoranalysis.image.core.object.label: Writes a unique ID (successive integer IDs) for each elements's voxels into a channel, and 0 for background.
LabelObjects(Function<T, ObjectMask>, BiFunction<T, ReadableTuple3i, T>) - Constructor for class org.anchoranalysis.image.core.object.label.LabelObjects
LabelObjects(Optional<UnaryOperator<T>>, Optional<Consumer<OverlappingObject<T>>>, Function<T, ObjectMask>, BiFunction<T, ReadableTuple3i, T>) - Constructor for class org.anchoranalysis.image.core.object.label.LabelObjects
labels() - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
LanguageUtilities - Class in org.anchoranalysis.core.value
lastConnectedTo(ContourList) - Method in class org.anchoranalysis.plugin.points.contour.ContourList
LastDirectories - Class in org.anchoranalysis.plugin.io.bean.descriptivename: Derives a name by taking the filename together with optionally several subdirectories names.
LastDirectories() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
LastDirectories(int) - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories: Creates for a particular number of subdirectories.
LastDirectoryAsPrefix - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer: Looks for the last directory-name, and removes it in favour of using it as a prefix on a filename
LastDirectoryAsPrefix() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
lastIndex(String) - Method in class org.anchoranalysis.io.generator.sequence.SequenceMemory
lastIndexOf(Object) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
lastIndexOf(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
Launch - Class in org.anchoranalysis.launcher: A command-line interface used for launching experiments
LauncherConfig - Class in org.anchoranalysis.launcher.config
LauncherConfig() - Constructor for class org.anchoranalysis.launcher.config.LauncherConfig
LaunchInteractiveBrowser - Class in org.anchoranalysis.browser.launcher: Command-line application for launching the anchor GUI application, otherwise known as interactive-browser.
LazyEvaluationStore<T> - Class in org.anchoranalysis.core.identifier.provider.store: Items are evaluated only when they are first needed.
LazyEvaluationStore(String) - Constructor for class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
leftSize() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
LegacyOutputEnabled - Class in org.anchoranalysis.plugin.mpp.experiment.bean.output: Deprecated.
Prefer another sub-class of OutputEnabledRules.
LegacyOutputEnabled() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.
length() - Method in class org.anchoranalysis.feature.results.ResultsVector
length() - Method in class org.anchoranalysis.spatial.point.Vector3d
LessThan - Class in org.anchoranalysis.math.relation
LessThan() - Constructor for class org.anchoranalysis.math.relation.LessThan
LessThanBean - Class in org.anchoranalysis.bean.shared.relation
LessThanBean() - Constructor for class org.anchoranalysis.bean.shared.relation.LessThanBean
LessThanEqualTo - Class in org.anchoranalysis.math.relation
LessThanEqualTo() - Constructor for class org.anchoranalysis.math.relation.LessThanEqualTo
LessThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation
LessThanEqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
LevelFromHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Calculates a level (a threshold-value) from a histogram.
LevelFromHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
LevelPerObjectBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Creates a channel with a level calculated for each object variously
LevelPerObjectBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
LevelPerObjectIndependently - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Creates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.
LevelPerObjectIndependently() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
LevelPerObjectNeighbors - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object: Calculates a threshold-level for each object collectively based on other objects
LevelPerObjectNeighbors() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
LevelResult - Class in org.anchoranalysis.plugin.image.intensity.level
LevelResult(int, ObjectMask, Histogram) - Constructor for class org.anchoranalysis.plugin.image.intensity.level.LevelResult
LevelResultCollection - Class in org.anchoranalysis.plugin.image.intensity.level
LevelResultCollection() - Constructor for class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
LevelResultCollectionFactory - Class in org.anchoranalysis.plugin.image.intensity.level
Limit<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Limits the number of input-objects to a certain hard-maximum
Limit - Class in org.anchoranalysis.plugin.io.bean.provider.file
Limit() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Limit
Limit() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.Limit
LimitWithDirectory - Class in org.anchoranalysis.plugin.io.bean.provider.file
LimitWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
LinearLeastSquaresEllipseFitter - Class in org.anchoranalysis.plugin.points.bean.fitter: Fits a set of points to an ellipse using a linear least squares method.
LinearLeastSquaresEllipseFitter() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
LinearLeastSquaresEllipsoidFitter - Class in org.anchoranalysis.plugin.points.bean.fitter: Fits an ellipsoid to points using a linear least squares approach
LinearLeastSquaresEllipsoidFitter() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
LinearLeastSquaresViaNormalEquationBase - Class in org.anchoranalysis.plugin.points.bean.fitter
LinearLeastSquaresViaNormalEquationBase() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
LineBoundCalculator - Class in org.anchoranalysis.plugin.mpp.bean.bound
LineBoundCalculator() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
LinePlot<T extends IndexGetter> - Class in org.anchoranalysis.plot.index: A line graph with 1 or more series, with an index on the x-axis.
LinePlot(String, String[], LinePlot.YValGetter<T>) - Constructor for class org.anchoranalysis.plot.index.LinePlot
LinePlot.YValGetter<T> - Interface in org.anchoranalysis.plot.index
LineSegment - Class in org.anchoranalysis.mpp.mark.points
LineSegment() - Constructor for class org.anchoranalysis.mpp.mark.points.LineSegment
LineSegment(Point3i, Point3i) - Constructor for class org.anchoranalysis.mpp.mark.points.LineSegment
list() - Method in class org.anchoranalysis.bean.StringList
list() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
list() - Method in class org.anchoranalysis.spatial.box.BoundedList: The collection of element with bounding-boxes.
ListBeanFactory<T> - Class in org.anchoranalysis.bean.xml.factory: Factory for creating a java.util.List of Beans
ListBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.ListBeanFactory
ListBeanFactory(CreateFromList<T>) - Constructor for class org.anchoranalysis.bean.xml.factory.ListBeanFactory
ListBoundCalculator - Class in org.anchoranalysis.plugin.mpp.bean.bound
ListBoundCalculator() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.ListBoundCalculator
listFeatures() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
listFeaturesSubset(int, int) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
listFrom2i(Mask) - Static method in class org.anchoranalysis.image.core.points.PointsFromMask
listFrom2i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of two-dimensional integer points from the entire object-mask
listFrom3d(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of points from the entire object-mask
listFrom3i(Mask) - Static method in class org.anchoranalysis.image.core.points.PointsFromMask
listFrom3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of three-dimensional integer points from the entire object-mask
listFromAllOutlines2i(ObjectCollection) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of points as three-dimensional integers from the outline of all objects in a collection
listFromOutline2i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of points as three-dimensional integers from the outline of an object-mask
listFromOutline3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A list of points as three-dimensional integers from the outline of an object-mask
listFromSlicesInsideBox3i(Mask, BoundingBox, int, int) - Static method in class org.anchoranalysis.image.core.points.PointsFromMask
listIterator() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
listIterator(int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
listOfBeans(String, HierarchicalConfiguration, Object) - Static method in class org.anchoranalysis.bean.xml.factory.HelperListUtilities: A list of instantiated bean objects from an XML configuration
listProbMap() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
ListSequence<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list: Populates a FeatureListElem with references to other features formed by one or two sequences of integers, so that all the features of the following pattern are contained in the list.
ListSequence() - Constructor for class org.anchoranalysis.feature.bean.list.ListSequence
ListUpdatableMarkSetCollection - Class in org.anchoranalysis.mpp.feature.mark
ListUpdatableMarkSetCollection() - Constructor for class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
ListWithThumbnails<T,S> - Class in org.anchoranalysis.plugin.image.feature.object: A list of items with an associated thumbnail-batch
ListWithThumbnails(List<T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
ListWithThumbnails(List<T>, ThumbnailBatch<S>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
loadBean(Path) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader: Creates a bean by loading an XML description from the filesystem
loadBean(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader: Creates a bean by loading an XML description from the filesystem
loadBeanAssociatedXml(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader: Creates a bean by loading an XML description from the filesystem
loadBeanLocalized(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader: Creates a bean by loading an XML description from the filesystem
localise(Path) - Method in class org.anchoranalysis.bean.AnchorBean: Called once after the bean is created, localising the bean to a path on the filesystem.
localise(Path) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
localise(Path) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
LocalisedBeanException - Exception in org.anchoranalysis.bean.xml.error: Combines many exceptions into a single exception, searching for a Cause and creating message string, incorporating the other strings
LocalisedBeanException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
LocalSlices - Class in org.anchoranalysis.image.voxel.kernel
LocalSlices(int, int, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.kernel.LocalSlices
log(String) - Method in interface org.anchoranalysis.core.log.MessageLogger
log(String) - Method in class org.anchoranalysis.core.log.NullMessageLogger
log(String) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
log(String) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
log(String) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
log(String) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
log(String) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
Log4JReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
Log4JReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
logDescription() - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
logEnd(JobDescription, JobState, boolean) - Method in class org.anchoranalysis.experiment.task.processor.JobStartStopLogger: Performs logging for when a job ends.
logFormatted(String, Object...) - Method in interface org.anchoranalysis.core.log.MessageLogger
logFormatted(String, Object...) - Method in class org.anchoranalysis.core.log.NullMessageLogger
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
Logger - Class in org.anchoranalysis.core.log: A logging-mechanism for both messages and errors.
Logger(MessageLogger) - Constructor for class org.anchoranalysis.core.log.Logger: Constructs with an error-reporter that writes into the message logger.
Logger(MessageLogger, ErrorReporter) - Constructor for class org.anchoranalysis.core.log.Logger
loggerForMonitor(ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
LoggingDestination - Class in org.anchoranalysis.experiment.bean.log: The destination(s) to which log-messages are sent.
LoggingDestination() - Constructor for class org.anchoranalysis.experiment.bean.log.LoggingDestination
LoggingFixture - Class in org.anchoranalysis.test: Fixtures to create loggers that don't output anything
logGraphDescription() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
logMemoryUsage(String, MessageLogger) - Static method in class org.anchoranalysis.core.system.MemoryUtilities
logStart(JobDescription) - Method in class org.anchoranalysis.experiment.task.processor.JobStartStopLogger: Performs logging for when a job starts.
LogUtilities - Class in org.anchoranalysis.core.log
LongestExtent - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
LongestExtent() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
LongestExtentWithin - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
LongestExtentWithin() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
LoopablePoints - Class in org.anchoranalysis.image.core.outline.traverser.visited: A set of points that can be looped, so as to form a path that ends with the same point that it begins with....
LoopablePoints(List<Point3i>, Point3i) - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
loopPointsLeft() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
loopPointsRight() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
lowerCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
lowerCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
lowerCountExistsThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Whether the count is less than a particular threshold.
LRUCache<K,V> - Class in org.anchoranalysis.core.cache: A cache that discards items that haven't being used recently or frequently (as per Guava's size-based eviction's defaults)
LRUCache(int, CheckedFunction<K, V, E>) - Constructor for class org.anchoranalysis.core.cache.LRUCache: Constructor

M

main(String[]) - Static method in class org.anchoranalysis.browser.launcher.LaunchInteractiveBrowser: Entry point for command-line application
main(String[]) - Static method in class org.anchoranalysis.launcher.Launch: Entry point for command-line application
makeOutputPath(String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Creates a full absolute path that completes the part of the path present in the outputter with an additional suffix.
makeOutputPath(String, String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Like OutputterChecked.makeOutputPath(String) but additionally adds an extension.
makePathAbsolute(String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
makePathAbsolute(String) - Method in interface org.anchoranalysis.io.output.path.prefixer.PathCreator: Generates a full path, given the final part (suffix) of a path.
makePathRelative(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
makePathRelative(Path) - Method in interface org.anchoranalysis.io.output.path.prefixer.PathCreator: Extracts a relative-file path, given the final part (suffix) of a path.
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
makeProposal(Optional<MarkCollection>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
makeProposal(Optional<MarksFromPartition>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelReplacePartition
makeProposal(Optional<MarksFromPartition>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel: Calculates the Energy for a proposal
makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
makeRGBStack(Stack) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
makeSureConfigured() - Method in class org.anchoranalysis.io.bioformats.ConfigureBioformatsLogging: Makes sure logging is configured
Manifest - Class in org.anchoranalysis.io.manifest: A manifest for a particular experiment, that may refer to the outputs from particular jobs, each with their own manifest.
Manifest() - Constructor for class org.anchoranalysis.io.manifest.Manifest
MANIFEST_FUNCTION - Static variable in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
MANIFEST_FUNCTION - Static variable in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
manifestCouplingDefinition(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
ManifestCouplingDefinition - Class in org.anchoranalysis.plugin.io.manifest
ManifestCouplingDefinition() - Constructor for class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
ManifestDescription - Class in org.anchoranalysis.io.manifest: A description of an entry (e.g.
ManifestDescription(String, String) - Constructor for class org.anchoranalysis.io.manifest.ManifestDescription
ManifestDeserializer - Interface in org.anchoranalysis.io.manifest.deserializer
ManifestDirectoryDescription - Class in org.anchoranalysis.io.manifest: A description of an directory in the manifest.
ManifestDirectoryDescription(String, String, SequenceType<?>) - Constructor for class org.anchoranalysis.io.manifest.ManifestDirectoryDescription
ManifestDirectoryDescription(Optional<ManifestDescription>, SequenceType<?>) - Constructor for class org.anchoranalysis.io.manifest.ManifestDirectoryDescription
ManifestGenerator - Class in org.anchoranalysis.io.generator.combined
ManifestGenerator() - Constructor for class org.anchoranalysis.io.generator.combined.ManifestGenerator
map(Function<T, S>) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence: Maps the existing object to another object, while retaining an identical confidence score.
map(UnaryOperator<ObjectMask>) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties: Maps the underlying object-mask to another object-mask, reusing the same properties object.
map(Optional<S>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Like Optional.map(java.util.function.Function<? super T, ? extends U>) but tolerates an exception in the mapping function, which is immediately thrown.
map(Stream<S>, Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a Stream.map(java.util.function.Function<? super T, ? extends R>) but accepts a function that can throw a checked-exception
map(CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Creates a new feature-list where each feature is the result of applying a map-function to an existing feature
map(CheckedFunction<ObjectMask, ObjectMask, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping each item to another.
mapBoth(Optional, Optional<V>, CheckedBiFunction<U, V, T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Mapping only occurs if both Optionals are non-empty (equivalent to a logical AND on the optionals)
mapBoundingBoxChangeExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Applies a function to map the bounding-box to a new-value (whose extent is expected to change in value)
mapBoundingBoxChangeExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping the bounding-box on each object (while maybe changing the extent).
mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Applies a function to map the bounding-box to a new-value (whose extent should be unchanged in value)
mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping the bounding-box on each object (whose extent should remain unchanged).
mapBoundingBoxPreserveExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Applies a function to map the bounding-box to a new-value (whose extent should be unchanged in value)
mapCalculator(UnaryOperator<FeatureCalculatorMulti<T>>) - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
mapChannel(CheckedUnaryOperator<Channel, OperationFailedException>) - Method in class org.anchoranalysis.image.core.stack.Stack: Produces a new stack with a particular mapping applied to each channel.
mapChannelIfSupported(int, BiFunction<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>, T>, Function<Channel, T>) - Method in class org.anchoranalysis.image.core.stack.ChannelMapper
mapChannelWithIndex(CheckedBiFunction<Channel, Integer, Channel, OperationFailedException>) - Method in class org.anchoranalysis.image.core.stack.Stack: Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available)
MapCreate<K,V> - Class in org.anchoranalysis.core.identifier.name: A tree map that creates a new item, if it doesn't already exist, after a GET operation
MapCreate(Supplier<V>) - Constructor for class org.anchoranalysis.core.identifier.name.MapCreate
MapCreate(Supplier<V>, Comparator<K>) - Constructor for class org.anchoranalysis.core.identifier.name.MapCreate
mapFrom(Iterable<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by mapping an Iterable to Feature
mapFrom(Iterable<T>, CheckedFunction<T, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by mapping an Iterable to ObjectMask
mapFromFiltered(Iterable<S>, Predicate<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by filtering an iterable and then mapping it to a feature
mapFromOptional(Iterable<T>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by mapping an Iterable to Optional
mapFromOptional(Iterator<T>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by mapping an Iterator to Optional
mapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by mapping integers (from a range) each to a ObjectMask
mapFromRange(int, int, IntFunction<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by mapping integers (from a range) each to a feature
mapFromRange(int, int, IntFunction<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection by mapping integers (from a range) each to a ObjectMask
mapFromRangeOptional(int, int, Class<? extends Exception>, CheckedIntFunction<Optional<Feature<T>>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by mapping integers (from a range) each to an optional feature
MapGroupToRow - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv: Maps Group (String) to a CSVRow
MapGroupToRow() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.csv.MapGroupToRow
mapIntStream(IntStream, Class<? extends Exception>, CheckedIntFunction<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Creates a new feature-list by mapping integers (from a range) each to an optional feature accepting a checked-exception
mapList(List<S>, ProgressReporter, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalProgress: Maps a list to new list, updating a progress-reporter for every element
mapListOptional(List<S>, ProgressReporter, CheckedFunction<S, Optional<T>, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalProgress: Maps a list to a new list, including only certain items, updating a progress-reporter for every element
mapRangeToList(int, int, IntFunction<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Creates a list of elements, where each element corresponds to an index in a range.
mapToInt(Stream<S>, Class<? extends Exception>, CheckedToIntFunction<S, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a Stream.mapToInt(java.util.function.ToIntFunction<? super T>) but accepts a function that can throw a checked-exception.
mapToList(Collection<S>, Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Like FunctionalList.mapToList(Object[], Function) but tolerates exceptions in the mapping function.
mapToList(Collection<S>, Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a collection to a list with each element derived from a corresponding element in the original collection.
mapToList(Stream<S>, Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a stream to a list with each element derived from a corresponding element in the original collection.
mapToList(CheckedFunction<ObjectMask, T, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new List after mapping each item to another type.
mapToList(S[], Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Like FunctionalList.mapToList(Object[], Function) but tolerates exceptions in the mapping function.
mapToList(S[], Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps an array to a list with each element derived from a corresponding element in the original array.
mapToListOptional(Collection<S>, Function<S, Optional<T>>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a collection to a list with each element in the original collection maybe producing an element in the output
mapToListOptional(CheckedFunction<ObjectMask, Optional<T>, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new List after mapping each item to another (optional) type
mapToListWithIndex(List<S>, BiFunction<S, Integer, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Maps a collection to a list with each element derived from a corresponding element in the original collection - and also letting the map function use an index.
mapToObj(IntStream, Class<? extends Exception>, CheckedIntFunction<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream: Performs a IntStream.mapToObj(java.util.function.IntFunction<? extends U>) but accepts a function that can throw a checked-exception.
mapToSortedSet(CheckedFunction<ObjectMask, T, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new SortedSet after mapping each item to another type.
Mark - Class in org.anchoranalysis.mpp.mark
Mark() - Constructor for class org.anchoranalysis.mpp.mark.Mark
Mark(Mark) - Constructor for class org.anchoranalysis.mpp.mark.Mark: Copy constructor
MarkAnd(S, T) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
MarkAnnotationDeleter - Class in org.anchoranalysis.annotation.io.mark
MarkAnnotationDeleter() - Constructor for class org.anchoranalysis.annotation.io.mark.MarkAnnotationDeleter
MarkAnnotationReader<T> - Class in org.anchoranalysis.annotation.io.mark: Reads a DualMarksAnnotation from a path on the filesystem.
MarkAnnotationReader(boolean) - Constructor for class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
MarkAnnotationWriter<T> - Class in org.anchoranalysis.annotation.io.mark
MarkAnnotationWriter() - Constructor for class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
markAsCompleted(boolean) - Method in class org.anchoranalysis.experiment.task.processor.JobState
markAsExecuting() - Method in class org.anchoranalysis.experiment.task.processor.JobState
markAsTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
MarkBounds - Class in org.anchoranalysis.mpp.bean.bound
MarkBounds() - Constructor for class org.anchoranalysis.mpp.bean.bound.MarkBounds
MarkBoundsDefine - Class in org.anchoranalysis.plugin.mpp.bean.bound
MarkBoundsDefine() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
MarkBoundsDefine(MarkBounds) - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
MarkBoundsProvider - Class in org.anchoranalysis.mpp.bean.provider
MarkBoundsProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarkBoundsProvider
MarkBoundsReference - Class in org.anchoranalysis.plugin.mpp.bean.bound
MarkBoundsReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
MarkCollection - Class in org.anchoranalysis.mpp.mark: A collection of marks, termed a configuration in marked-point-processes academic literature.
MarkCollection() - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
MarkCollection(List) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
MarkCollection(Stream) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
MarkCollection(Mark) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
MarkCollectionDeserializer - Class in org.anchoranalysis.mpp.io.marks
MarkCollectionDeserializer() - Constructor for class org.anchoranalysis.mpp.io.marks.MarkCollectionDeserializer
MarkCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer: Proposes an entire collection (confguration) of marks
MarkCollectionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkCollectionProposer
MarkCollectionProvider - Class in org.anchoranalysis.mpp.bean.provider: Provides a collection of marks
MarkCollectionProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarkCollectionProvider
MarkConicFactory - Class in org.anchoranalysis.mpp.mark.conic
MarkDistance - Class in org.anchoranalysis.mpp.bean.mark
MarkDistance() - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkDistance
MarkDistanceAbstractPosition - Class in org.anchoranalysis.plugin.mpp.bean.distance
MarkDistanceAbstractPosition() - Constructor for class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceAbstractPosition
MarkDistanceRadii - Class in org.anchoranalysis.plugin.mpp.bean.distance
MarkDistanceRadii() - Constructor for class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceRadii
MarkEllipseCircumEstimate - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region: Estimates the circumference of an ellipse based upon finding the area of the shell, and dividing // by the ShellRad
MarkEllipseCircumEstimate() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.MarkEllipseCircumEstimate
MarkEllipseFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
MarkEllipseFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
MarkEllipseSimple - Class in org.anchoranalysis.plugin.mpp.bean.proposer.split
MarkEllipseSimple() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
MarkEllipsoidFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
MarkEllipsoidFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
MarkEvaluator - Class in org.anchoranalysis.mpp.feature.bean.mark
MarkEvaluator() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
MarkFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
MarkFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkFactory
markFactoryContext() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
MarkFactoryContext - Class in org.anchoranalysis.mpp.segment.kernel
MarkFactoryContext(MarkWithIdentifierFactory) - Constructor for class org.anchoranalysis.mpp.segment.kernel.MarkFactoryContext
MarkFromCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer
MarkFromCollectionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkFromCollectionProposer
MarkFromCollectionProposerUnary - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
MarkFromCollectionProposerUnary() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
MarkMergeProposer - Class in org.anchoranalysis.mpp.bean.proposer
MarkMergeProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
MarkMergeProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.merge
MarkMergeProposerReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
markNoProposal(ProposerFailureDescription) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
MarkPairCollection - Class in org.anchoranalysis.mpp.feature.mark: A pair collection where the underlying type is a simple IdentifiablePair
MarkPairCollection() - Constructor for class org.anchoranalysis.mpp.feature.mark.MarkPairCollection
MarkPointListFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
MarkPointListFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkPointListFactory
MarkProposer - Class in org.anchoranalysis.mpp.bean.proposer
MarkProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkProposer
MarkProposerFromList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
MarkProposerFromList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
MarkProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
MarkProposerReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
MarkProposerStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy: Annotates each image with a mark
MarkProposerStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
MarkProposerUnary - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
MarkProposerUnary() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
MarkProviderPointsFitterFromConvexHull - Class in org.anchoranalysis.plugin.points.bean.mark.provider.single
MarkProviderPointsFitterFromConvexHull() - Constructor for class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
MarkRegion - Class in org.anchoranalysis.mpp.bean.mark
MarkRegion() - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkRegion
marks() - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks: The marks associated with the annotation
marks() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
marks() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
MARKS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories: Where collections of marks are typically placed in a define-experiment output
MarksAsUniqueValueGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
MarksAsUniqueValueGenerator(Dimensions, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
marksAt(Point3d, RegionMap, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
MarksComparer - Class in org.anchoranalysis.plugin.annotation.bean.comparer
MarksComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
marksDeriver() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
MarksFlattenedGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
MarksFlattenedGenerator(DrawObject, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksFlattenedGenerator
MarksFromEnergyHelper - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
marksFromMemo(MemoCollection) - Static method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MarksFromEnergyHelper
marksFromOverlays(ColoredOverlayCollection) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
marksFromOverlays(OverlayCollection) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
MarksFromPartition - Class in org.anchoranalysis.plugin.mpp.segment.optimization: A subset of a marks (as extracted during a partition)
MarksFromPartition(MarkCollection, PartitionedMarks) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition
MarksGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
MarksGenerator(DrawObject, IdentifierGetter<Overlay>) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksGenerator
MarksGenerator(DrawObject, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksGenerator
MarksGeneratorBase - Class in org.anchoranalysis.mpp.io.marks.generator
MarksGeneratorBase(DrawOverlay, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
marksNew() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
MarkSplitProposer - Class in org.anchoranalysis.mpp.bean.proposer
MarkSplitProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkSplitProposer
MarkSplitProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.split
MarkSplitProposerReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
MarksWithDisplayStack - Class in org.anchoranalysis.mpp.io.marks
MarksWithDisplayStack(MarkCollection, DisplayStack) - Constructor for class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
MarksWithEnergyBreakdown - Class in org.anchoranalysis.mpp.feature.energy.marks: Marks with both the total energy and a breakdown by clique
MarksWithEnergyBreakdown(MarksWithTotalEnergy) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
MarksWithEnergyBreakdown(MarksWithTotalEnergy, EnergySavedInd, EnergySavedPairs, EnergySavedAll) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
MarksWithTotalEnergy - Class in org.anchoranalysis.mpp.feature.energy.marks: A collection of marks with an associated (total) energy.
MarksWithTotalEnergy(MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
MarkWithIdentifierFactory - Class in org.anchoranalysis.mpp.bean.mark
MarkWithIdentifierFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
MarkWithIdentifierFactory(MarkFactory) - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
MarkWithPosition - Class in org.anchoranalysis.mpp.mark
MarkWithPosition() - Constructor for class org.anchoranalysis.mpp.mark.MarkWithPosition
MarkWithPosition(MarkWithPosition) - Constructor for class org.anchoranalysis.mpp.mark.MarkWithPosition
MarkWithPositionAndSingleRadius - Class in org.anchoranalysis.mpp.mark.conic: Base-class for a conic that has a single radius (circle, sphere etc.)
MarkWithPositionAndSingleRadius() - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
MarkWithPositionAndSingleRadius(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Constructor with a bound on the radius
MarkWithPositionAndSingleRadius(MarkWithPositionAndSingleRadius) - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Copy constructor
mask(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
Mask - Class in org.anchoranalysis.image.core.mask: A channel that is restricted to two values (ON and OFF) so as to act like a mask.
Mask(Channel) - Constructor for class org.anchoranalysis.image.core.mask.Mask: Creates a mask from an existing channel using default values for OFF (0) and ON (255)
Mask(Channel, BinaryValues) - Constructor for class org.anchoranalysis.image.core.mask.Mask: Creates a mask from an existing channel
Mask(Dimensions, BinaryValues) - Constructor for class org.anchoranalysis.image.core.mask.Mask: Creates a new empty mask of particular dimensions and with particular binaryvalues
Mask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.core.mask.Mask: Creates a mask from an existing binary-voxels using default image resolution
Mask(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.mask.Mask: Creates a mask from an existing binary-voxels and a specific image resolution.
MaskAnd - Class in org.anchoranalysis.image.core.mask.combine
MaskAsSingleObject<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculate a feature, treating a mask as a single-object on the energy-stack
MaskAsSingleObject() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
MaskComparer - Class in org.anchoranalysis.plugin.annotation.bean.comparer
MaskComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
MaskFactory - Class in org.anchoranalysis.image.core.mask: Helper routines to create new instances of Mask
MaskFromObjects - Class in org.anchoranalysis.image.core.mask: Creates a mask from one or more objects.
MaskIfHighLow - Class in org.anchoranalysis.image.core.mask.combine
MaskIntersectionAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
MaskIntersectionAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
MaskInverter - Class in org.anchoranalysis.image.core.mask: Inverts masks and objects
MaskOr - Class in org.anchoranalysis.image.core.mask.combine
MaskProvider - Class in org.anchoranalysis.image.bean.provider
MaskProvider() - Constructor for class org.anchoranalysis.image.bean.provider.MaskProvider
MaskProviderUnary - Class in org.anchoranalysis.image.bean.provider
MaskProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.MaskProviderUnary
masks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
maskScaledXY(Dimensions, RegionMembershipWithFlags, BinaryValuesByte, double) - Method in class org.anchoranalysis.mpp.mark.Mark
MaskXor - Class in org.anchoranalysis.image.core.mask.combine
match(int, int) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Helper method to record a matching between worker w and job j.
match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegEx: Returns an array of string components it matches successfully, or empty() if it cannot match
match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExList
match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
match(VoxelDataType) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate: A predicate condition for an object to be kept in the collection
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
Match - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
Match() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
matchDirectories() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
MatchedAppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend: An append CSV and corresponding match value
MatchedAppendCsv() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
MatchedObject - Class in org.anchoranalysis.image.core.object: An object with associated matches.
MatchedObject(ObjectMask, ObjectCollection) - Constructor for class org.anchoranalysis.image.core.object.MatchedObject
MatcherIntersectionHelper - Class in org.anchoranalysis.plugin.image.bean.object.match
matchingFilesForDirectory(Path, InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
matchingFilesForDirectory(Path, InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
matchIntersectingObjects(ObjectCollection, ObjectCollection) - Static method in class org.anchoranalysis.plugin.image.bean.object.match.MatcherIntersectionHelper
max() - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
max(boolean) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
max(double) - Method in class org.anchoranalysis.spatial.point.Point3d: Element-wise maximum between this point and a scalar
max(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Element-wise maximum between this point and a scalar
max(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Element-wise maximum between this point and another
max(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Point3d: Element-wise maximum between this point and another
Max - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Max() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Max
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType
MAX_VALUE - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
MAX_VALUE_INT - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType
MAX_VALUE_INT - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType
maxAsInt(ToIntFunction<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Finds the maximum value of a function applied to each object in the collection.
MaxDensityKernel3 - Class in org.anchoranalysis.image.voxel.kernel.density: Erosion with a 3x3 or 3x3x3 kernel
MaxDensityKernel3(BinaryValuesByte, boolean, boolean, int) - Constructor for class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
maxDistanceToClosestPoint(ContiguousVoxelPath, Point3i) - Static method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceToContiguousPath: The maximum-distance of a point to the closest point on the path
maxDistanceToHeadTail(ContiguousVoxelPath, Point3i) - Static method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceToContiguousPath
MaxFeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
MaxFeatureIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MaxFeatureIntersectingObjects
Maximum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: The maximum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Maximum<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
Maximum() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
Maximum() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Maximum
MAXIMUM - org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType
MaximumIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
MaximumIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MaximumIntensityProjection
MaximumNumberContourVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice: Maximum number of voxels on any slice's contour (edge voxels) across all slices.
MaximumNumberContourVoxelsOnSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberContourVoxelsOnSlice
MaximumNumberVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice: Maximum number of voxels in the object-mask across all slices.
MaximumNumberVoxelsOnSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberVoxelsOnSlice
MaxIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel
MaxIntensity() - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
MaxIntensityBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer.max: The buffer used when making a maximum-intensity projection
MaxIntensityBuffer(Extent, VoxelsFactoryTypeBound<T>) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer
MaxIntensityBufferByte - Class in org.anchoranalysis.image.voxel.buffer.max
MaxIntensityBufferByte(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferByte
MaxIntensityBufferFloat - Class in org.anchoranalysis.image.voxel.buffer.max
MaxIntensityBufferFloat(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferFloat
MaxIntensityBufferInt - Class in org.anchoranalysis.image.voxel.buffer.max
MaxIntensityBufferInt(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferInt
MaxIntensityBufferShort - Class in org.anchoranalysis.image.voxel.buffer.max
MaxIntensityBufferShort(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferShort
MaxIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram
MaxIntensityFromHistogram() - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
MaxIntensityProjectionPair - Class in org.anchoranalysis.mpp.overlap
MaxIntensityProjectionPair(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, RegionMembershipWithFlags, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.overlap.MaxIntensityProjectionPair
MaxNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
MaxNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.MaxNonZero
maxOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
MaxOverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
MaxOverlapRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
MaxOverlapRatio(double) - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
MaxRatioRadii - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
MaxRatioRadii() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.MaxRatioRadii
MaxSliceArea - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
MaxSliceArea() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MaxSliceArea
MaxTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MaxTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxTwoChannels
maxValue() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: The maximum value this type can represent.
MaxWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MaxWithConstant - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
MaxWithConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxWithConstant
MaxWithConstant() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
maybeAddOutputs() - Method in class org.anchoranalysis.launcher.options.outputs.ProcessOutputOptions: Processes any options that have been defined to add/remove change the outputs that are enabled.
maybeAddPointToClosestEnd(Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath: Adds the point to the closest end of the path....
maybeCreateUserFriendlyException(Throwable) - Static method in class org.anchoranalysis.bean.xml.error.HelperFriendlyExceptions: Possibly replaces an exception with a more user-friendly description
maybeDistanceCondition() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
maybeSubdirectory(Optional<String>, ManifestDirectoryDescription, boolean) - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Optionally creates a new context like with InputOutputContext.subdirectory(java.lang.String, org.anchoranalysis.io.manifest.ManifestDirectoryDescription, boolean) but only if a directory-name is defined
mean() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
mean() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Calculates the mean
mean() - Method in class org.anchoranalysis.math.histogram.Histogram
mean() - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
mean() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
mean(double) - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Calculates the mean
mean(double) - Method in class org.anchoranalysis.math.histogram.Histogram: calculates the mean after raising each histogram value to a power i.e.
mean(double, double) - Method in class org.anchoranalysis.math.histogram.Histogram: calculates the mean of (histogramVal - subtractVal)^power
Mean - Class in org.anchoranalysis.feature.bean.results: The mean of the results from a particular feature.
Mean - Class in org.anchoranalysis.image.feature.histogram
Mean<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list: Arithmetic mean of a list of features
Mean() - Constructor for class org.anchoranalysis.feature.bean.results.Mean
Mean() - Constructor for class org.anchoranalysis.image.feature.histogram.Mean
Mean() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Mean
MeanAcrossObjects<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates the mean of a feature applied to each connected component
MeanAcrossObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.MeanAcrossObjects
meanAndReset() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Calculate the mean and then reset to zero
meanAndReset() - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection: Calculate the mean of each item and reset to zero.
meanExecutionTimeFailed() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: Mean execution-time of failed jobs in milliseconds.
meanExecutionTimeSuccess() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: Mean execution-time of successfully-completed jobs in milliseconds.
MeanFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
MeanFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.MeanFilter2D
MeanFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
MeanFromAll() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
MeanGeometric<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
MeanGeometric() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
meanGreaterEqualTo(int) - Method in class org.anchoranalysis.math.histogram.Histogram
MeanIntensityBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer.mean
MeanIntensityBuffer(VoxelsFactoryTypeBound<T>, Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer: Simple constructor since no preprocessing is necessary.
MeanIntensityByteBuffer - Class in org.anchoranalysis.image.voxel.buffer.mean
MeanIntensityByteBuffer(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityByteBuffer: Simple constructor since no preprocessing is necessary.
MeanIntensityDifference - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
MeanIntensityDifference() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
MeanIntensityDifference(double) - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
MeanIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
MeanIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MeanIntensityProjection
MeanIntensityShortBuffer - Class in org.anchoranalysis.image.voxel.buffer.mean
MeanIntensityShortBuffer(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityShortBuffer: Simple constructor since no preprocessing is necessary.
meanNonZero() - Method in class org.anchoranalysis.math.histogram.Histogram
meanOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
MeanRaisedToPower - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: The mean of the intensity raised to power
MeanRaisedToPower() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
MeanThreeChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Creates a new channel that is the mean of three input channels
MeanThreeChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MeanThreeChannels
meanXY() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
Median - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Applies a median-filter with square kernel
Median - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Median() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
Median() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Median
MedianFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
MedianFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter2D
MedianFilter3D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
MedianFilter3D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter3D
membershipForIndex(int) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
membershipWithFlagsForIndex(int) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
MemoCollection - Class in org.anchoranalysis.mpp.feature.mark: A collection of memoized marks on which energies can be derived.
MemoCollection() - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoCollection
MemoCollection(EnergySavedInd, EnergyStackWithoutParams, MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoCollection
MemoCollection(MemoCollection) - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoCollection
MemoForIndex - Interface in org.anchoranalysis.mpp.mark.voxelized.memo
MemoList - Class in org.anchoranalysis.mpp.feature.mark
MemoList() - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoList
MemoryUsageReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
MemoryUsageReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
MemoryUtilities - Class in org.anchoranalysis.core.system
merge() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate: Merges
merge(TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
merge(ObjectCollection) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger: Merges all the objects together that are found in a collection
merge(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger: Merges two objects together
MergeBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: A base class for algorithms that merge object-masks
MergeBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
MergeBase.MergeObjects - Interface in org.anchoranalysis.plugin.image.bean.object.provider.merge
mergeBoundingBoxes(Stream<ObjectMask>) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger: Merges all the bounding boxes of a stream of objects.
mergeBoundingBoxes(Stream<BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundingBoxMerger: Merges all the bounding boxes in a stream.
mergeBoundingBoxes(ObjectCollection) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger: Merges all the bounding boxes of a collection of objects.
MergeCandidate - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy
MergeCandidate(ContiguousVoxelPath, ContiguousVoxelPath, Point3i, Point3i) - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
Merged - Class in org.anchoranalysis.image.feature.bean.object.pair: Evaluates the first-object in a pair only
Merged() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Merged
Merged(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Merged
MERGED - org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
MergedPairsFeatures - Class in org.anchoranalysis.image.feature.session.merged: The list of features that can be used in a PairsTableCalculator
MergedPairsFeatures(FeatureList<FeatureInputPairObjects>) - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures: Creates to only calculate pair features.
MergedPairsFeatures(FeatureList<FeatureInputStack>, FeatureList<FeatureInputSingleObject>, FeatureList<FeatureInputPairObjects>) - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures: Creates with features for single, pair and image as a whole.
MergedPairsInclude - Class in org.anchoranalysis.image.feature.session.merged
MergedPairsInclude() - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
MergedPairsInclude(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
MergeGraph - Class in org.anchoranalysis.plugin.image.object.merge: A graph that stores each object as a vertex, where edges represent a neighborhood relation.
MergeGraph(PayloadCalculator, UpdatableBeforeCondition, Optional<UnitConverter>, AssignPriority, Logger, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.MergeGraph: Constructor
MergeGreedyToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Naive greedy merge strategy when any two neighboring objects are merged if it increases a feature.
MergeGreedyToIncreaseObjectFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
MergeLists - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
MergeLists() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
MergeMarkEllipse - Class in org.anchoranalysis.plugin.mpp.bean.proposer.merge
MergeMarkEllipse() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
mergeMultiplex(ObjectCollection, MergeBase.MergeObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase: Merges either in a container, or altogether
mergeObjects(ObjectCollection) - Method in interface org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase.MergeObjects
MergePairs - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges objects if a pair feature value satisfies a condition
MergePairs() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
MergeSpatialClusters - Class in org.anchoranalysis.plugin.ml.bean.cluster: Merges spatially-adjacent objects using the DBScan clustering algorithm.
MergeSpatialClusters() - Constructor for class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
MergeStrategy - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy
MergeStrategy(int) - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeStrategy
MergeToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges neighboring objects if it results in an increase in the average feature-value calculated on each single object
MergeToIncreaseObjectFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
MergeTwoCollectionsItemwise - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Merges itemwise objects from two collections.
MergeTwoCollectionsItemwise() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
mergeViaZeroCheck(Channel, Channel, VoxelDataType, double) - Static method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero: Creates a new channel which is a merged version of two input channels according to rules.
MergeWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Base class for object-merging strategies that involve calculating a feature.
MergeWithFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
MergeWithOptionalDistanceConstraint - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge: Expands MergeBase by optionally imposing a maximum-distance requirement between objects that are possibly merged.
MergeWithOptionalDistanceConstraint() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
messageLogger() - Method in class org.anchoranalysis.core.log.Logger: Where messages logged to
MessageLogger - Interface in org.anchoranalysis.core.log: Logs messages (strings) somewhere.
MessageLoggerList - Class in org.anchoranalysis.experiment.log
MessageLoggerList(Stream<StatefulMessageLogger>) - Constructor for class org.anchoranalysis.experiment.log.MessageLoggerList
metadataAggregated(NamedFeatureStore<FeatureInputResults>) - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata: Derives metadata for the aggregated CSV output, if enabled.
metadataNonAggregated() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata: Derives metadata for the non-aggregated CSV output.
MICRO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
midpoint() - Method in class org.anchoranalysis.spatial.box.BoundingBox: A mid-point in the bounding box, in the exact half way point between (crnr+extent)/2.
midPointBetween(Point3d, Point3d) - Static method in class org.anchoranalysis.spatial.point.Point3d
min() - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
min(boolean) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
min(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Point3d: Element-wise minimum between this point and another
min(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i: Element-wise minimum between this point and another
min(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Point3d: Element-wise minimum between this point and another
Min - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Min() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Min
MIN_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
MIN_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType
minArea() - Method in class org.anchoranalysis.mpp.overlap.MaxIntensityProjectionPair
minAsInt(ToIntFunction<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Finds the minimum value of a function applied to each object in the collection.
minDistanceMaxToHeadTail(Point3i, List<ContiguousVoxelPath>) - Static method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.FindMinimumDistance: The maximum-distance of a point to the closest contiguous-path
MinFeatureAsIndividual - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
MinFeatureAsIndividual() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.MinFeatureAsIndividual
MinFeatureIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
MinFeatureIntersectingObjectsAboveThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MinFeatureIntersectingObjectsAboveThreshold
MinimaImposition - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
MinimaImposition() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImposition
MinimaImpositionGrayscaleReconstruction - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
MinimaImpositionGrayscaleReconstruction() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
MinimalExecutionTimeStatsReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
MinimalExecutionTimeStatsReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
Minimum - Class in org.anchoranalysis.image.feature.bean.object.pair: Ratio of first-object to second-object in a pair
Minimum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: The minimum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Minimum<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
Minimum() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Minimum
Minimum() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
Minimum() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Minimum
Minimum(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Minimum
MINIMUM - org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType
MinimumDistanceByDimension - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance: The minimum distance in any one particular axis-aligned direction (i.e.
MinimumDistanceByDimension() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.MinimumDistanceByDimension
MinimumFilter - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider
MinimumFilter() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.MinimumFilter
minNumPoints() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
minOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
MinTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MinTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinTwoChannels
minVal - Variable in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
minValue() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: The minimum value this type can represent.
MinWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MinWithConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinWithConstant
MockFeatureWithCalculation - Class in org.anchoranalysis.test.feature.plugins.mockfeature: A feature that returns the number-of-voxels in an object by using am internal mock-calculation.
MockFeatureWithCalculation() - Constructor for class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculation
MockFeatureWithCalculationFixture - Class in org.anchoranalysis.test.feature.plugins.mockfeature: Creates a mock-feature which used a mock FeatureCalculation under the hood
Mode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Mode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Mode
MonitoredSequentialExecutor<T> - Class in org.anchoranalysis.experiment.task.processor: Runs executes sequence of jobs/tasks/whatever monitoring various pieces of information - how many have run? - how many successful/failed? - how long did execution take? - etc.
MonitoredSequentialExecutor(Predicate<T>, Function<T, String>, Optional<MessageLogger>, boolean) - Constructor for class org.anchoranalysis.experiment.task.processor.MonitoredSequentialExecutor
MontageSlices - Class in org.anchoranalysis.plugin.imagej.bean.stack.provider
MontageSlices() - Constructor for class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
moreThanOneObj() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner: Can more than one object exist?
moreThanOneObj() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
moreThanOneObj() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
MorphologicalDilation - Class in org.anchoranalysis.image.voxel.object.morphological
MorphologicalErosion - Class in org.anchoranalysis.image.voxel.object.morphological
MorphologicalIterations - Class in org.anchoranalysis.plugin.image.feature.bean.morphological: Specifies a certain number of iterations of the morphological operations of dilation and erosion
MorphologicalIterations() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
MorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider: Applies an ImageJ (2D) morphological operation to each slice
MorphologicalOperation() - Constructor for class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
MorphologicalOperatorBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Base class for performing morphological operations
MorphologicalOperatorBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
moveAcceptedToAvailable(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
moveAvailableToAccepted(Set) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
MovieFromSlices - Class in org.anchoranalysis.plugin.image.task.bean.slice
MovieFromSlices() - Constructor for class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
MPPBean<T> - Class in org.anchoranalysis.mpp.bean
MPPBean() - Constructor for class org.anchoranalysis.mpp.bean.MPPBean
MPPInitParams - Class in org.anchoranalysis.mpp.bean.init
MPPInitParams(ImageInitParams, SharedObjects) - Constructor for class org.anchoranalysis.mpp.bean.init.MPPInitParams
MPPInitParamsFactory - Class in org.anchoranalysis.mpp.io.input
MPPProvider<T,S> - Class in org.anchoranalysis.mpp.bean.provider
MPPProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MPPProvider
Mser - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Applies the MSER algorithm from imglib2
Mser() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
mult(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
multConstant(double) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
MultiBufferSized - Class in org.anchoranalysis.plugin.io.multifile.buffer
MultiBufferSized(Stack, SizeExtents) - Constructor for class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
MultiFileReader - Class in org.anchoranalysis.plugin.io.bean.stack.reader
MultiFileReader() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
MultiFileReaderOpenedRaster - Class in org.anchoranalysis.plugin.io.multifile
MultiFileReaderOpenedRaster(StackReader, ParsedFilePathBag) - Constructor for class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
MultiInput - Class in org.anchoranalysis.mpp.io.input
MultiInput(String, ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.MultiInput
MultiInput(ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.MultiInput
MultiInputManager - Class in org.anchoranalysis.mpp.io.bean.input
MultiInputManager() - Constructor for class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
MultiInputManager(String, InputManager<? extends ProvidesStackInput>) - Constructor for class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
MultiInputManagerQuick - Class in org.anchoranalysis.plugin.quick.bean.input: A multi-input manager that makes various assumptions, so it can be more quickly specified.
MultiInputManagerQuick() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
MultiInputSubMap<T> - Interface in org.anchoranalysis.mpp.io.input: a sub-item of multi-input which: 1.
MultiLevelAnd - Class in org.anchoranalysis.io.output.enabled.multi: Outputs are enabled if they are contained in both of two MultiLevelOutputEnableds.
MultiLevelAnd(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd: Creates using two MultiLevelOutputEnableds.
MultiLevelBinary - Class in org.anchoranalysis.io.output.enabled.multi
MultiLevelBinary(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
MultiLevelNot - Class in org.anchoranalysis.io.output.enabled.multi: The complement of an existing MultiLevelOutputEnabled where disabled outputs are enabled, and vice-versa.
MultiLevelNot(MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
MultiLevelOr - Class in org.anchoranalysis.io.output.enabled.multi: Outputs are enabled if they are contained in either of two MultiLevelOutputEnableds.
MultiLevelOr(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr: Creates using two MultiLevelOutputEnableds.
MultiLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.multi: Whether an output is enabled or not in a context of hierarchy of different rules for outputting.
MultiLevelRecordedOutputs - Class in org.anchoranalysis.io.output.recorded: Like RecordedOutputs but accepts two levels, first and second, like in a MultiLevelRecordedOutputs.
MultiLevelRecordedOutputs() - Constructor for class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
MultiName - Interface in org.anchoranalysis.feature.io.name: A name that that uniquely identifies an entity, and is composed of two parts.
MultiNameFactory - Class in org.anchoranalysis.feature.io.name: Creates MultiName.
MultipleComparer - Class in org.anchoranalysis.annotation.io.bean.comparer: Allows comparison of an annotation with multiple other entities.
MultipleComparer() - Constructor for class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
MultipleFileTypeGenerator<T> - Interface in org.anchoranalysis.io.generator: A Generator that creates multiple different file-types.
multipleProcessors(int, int) - Static method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan: Creates a plan for a multiple CPU-processors
multipleSeries() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
multiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: Multiplexes between the selective and permissive writers based on a flag.
Multiply<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
Multiply() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
multiplyBy(double) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Multiplies the value of all voxels by a factor
multiplyBy(ObjectMask, double) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Multiplies each voxel by constant factor but only for voxels inside an object-mask
MultiplyByConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
MultiplyByConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
MultiplyByConstant(Feature<T>, double) - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
MultiplyConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MultiplyConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyConstant
MultiplyTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
MultiplyTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyTwoChannels
MutableDirectory - Class in org.anchoranalysis.io.manifest.directory: An entry for a directory in the manifest, to which outputs and sub-directories can be later added.
MutableDirectory() - Constructor for class org.anchoranalysis.io.manifest.directory.MutableDirectory
MutableDirectory(MutableDirectory) - Constructor for class org.anchoranalysis.io.manifest.directory.MutableDirectory

N

name() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
name() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
name() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
name() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
name() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
name() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
name() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
NamedBean<T extends AnchorBean<?>> - Class in org.anchoranalysis.bean: A bean with an associated textual name.
NamedBean() - Constructor for class org.anchoranalysis.bean.NamedBean
NamedBean(String, T) - Constructor for class org.anchoranalysis.bean.NamedBean
NamedChannel - Class in org.anchoranalysis.plugin.image.task.grouped
NamedChannel(String, Channel) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
NamedChannels - Class in org.anchoranalysis.plugin.io.bean.input.channel: An image viewed as a named set of channels
NamedChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
NamedChannelsAppend - Class in org.anchoranalysis.plugin.io.bean.input.channel
NamedChannelsAppend() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
NamedChannelsBase - Class in org.anchoranalysis.plugin.io.bean.input.channel: Parent for all the NamedChannels classes
NamedChannelsBase() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsBase
NamedChannelsQuick - Class in org.anchoranalysis.plugin.quick.bean.input: A particular type of NamedChannels which allows easier input of data, making several assumptions.
NamedChannelsQuick() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
NamedFeatureCalculateException - Exception in org.anchoranalysis.feature.calculate: A feature-calculation exception that occurs in a particular named feature, or else a general message of failure.
NamedFeatureCalculateException(Exception) - Constructor for exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Creates with a calculation error that doesn't pertain to any particular feature.
NamedFeatureCalculateException(String) - Constructor for exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Creates with a general failure message that doesn't pertain to any particular feature.
NamedFeatureCalculateException(String, String) - Constructor for exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Creates with a failure message associated with a particular feature.
NamedFeatureCalculatorMulti<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.evaluator: A FeatureCalculatorMulti with associated feature-names
NamedFeatureCalculatorMulti(FeatureCalculatorMulti<T>, FeatureNameList) - Constructor for class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
NamedFeatureStore<T extends FeatureInput> - Class in org.anchoranalysis.feature.list
NamedFeatureStore() - Constructor for class org.anchoranalysis.feature.list.NamedFeatureStore
NamedFeatureStoreFactory - Class in org.anchoranalysis.feature.list
NamedFiles - Class in org.anchoranalysis.plugin.io.bean.input.files: File-paths
NamedFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
NamedFiles(FilesProvider) - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
NamedPath - Class in org.anchoranalysis.io.output.path.prefixer: A path and associated name.
NamedPath(String, Path) - Constructor for class org.anchoranalysis.io.output.path.prefixer.NamedPath
NamedProvider<T> - Interface in org.anchoranalysis.core.identifier.provider: A collection of named-elements that provides an element for a given name.
NamedProviderBridge<S,T> - Class in org.anchoranalysis.core.identifier.provider
NamedProviderBridge(NamedProvider<S>, CheckedFunction<S, T, ? extends Exception>) - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
NamedProviderBridge(NamedProvider<S>, CheckedFunction<S, T, ? extends Exception>, boolean) - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
NamedProviderCombine<T> - Class in org.anchoranalysis.core.identifier.provider
NamedProviderCombine() - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
NamedProviderGetException - Exception in org.anchoranalysis.core.identifier.provider
NamedProviderGetException(String, Throwable) - Constructor for exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
NamedProviderOutputter<T> - Class in org.anchoranalysis.io.generator.collection: Outputs entities from a NamedProvider into a directory using the names of each entity for a corresponding generated file.
NamedProviderOutputter(NamedProvider<T>, Generator<T>, OutputterChecked) - Constructor for class org.anchoranalysis.io.generator.collection.NamedProviderOutputter
NamedProviderStore<T> - Interface in org.anchoranalysis.core.identifier.provider.store: A provider, in which items can also be added.
NamedStacks - Class in org.anchoranalysis.image.core.stack: A set of image-stacks each with a name
NamedStacks() - Constructor for class org.anchoranalysis.image.core.stack.NamedStacks
NamedStacksSupplier - Interface in org.anchoranalysis.image.core.stack
NamedStacksUniformSize - Class in org.anchoranalysis.image.core.stack: Like a @{link NamedStacks but enforces a condition that all stacks must have the same dimensions
NamedStacksUniformSize() - Constructor for class org.anchoranalysis.image.core.stack.NamedStacksUniformSize
nameForPropValue(Double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
nameForPropValue(Double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
nameForPropValue(Integer) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
nameForPropValue(Integer) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
nameForPropValue(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
nameForPropValue(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
nameForPropValue(T) - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty: Converts a particular value to a string representation
nameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle: Constructs a full name from the output format string and an index
nameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
nameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
NameValue<T> - Interface in org.anchoranalysis.core.identifier.name: An object that has an associated textual name and value
NameValueSet<T> - Class in org.anchoranalysis.core.identifier.provider
NameValueSet() - Constructor for class org.anchoranalysis.core.identifier.provider.NameValueSet
NameValueSet(Iterable<? extends NameValue<T>>) - Constructor for class org.anchoranalysis.core.identifier.provider.NameValueSet
NANO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
negative() - Method in class org.anchoranalysis.image.core.orientation.Orientation
negative() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
negative() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
negative() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
negative() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
negative() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
NeighborGraph - Class in org.anchoranalysis.image.voxel.neighborhood
Neighborhood - Interface in org.anchoranalysis.image.voxel.neighborhood
NeighborhoodCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition: A condition placed to determine if two objects could be potential neighbors are not (i.e.
NeighborhoodCondition(boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
NeighborhoodFactory - Class in org.anchoranalysis.image.voxel.neighborhood: Creates either a big voxel-neighborhood or a small voxel-neighborhood.
newlinesBeforeError() - Method in class org.anchoranalysis.launcher.config.LauncherConfig: if true, then some extra newlines are inserted before error messages
newTemplateMark() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
next() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
nextIndex(int) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncomplete
nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
nextValue() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
NoAnnealing - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
NoAnnealing() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.annealing.NoAnnealing
noInterpolation() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
None - Class in org.anchoranalysis.image.bean.interpolator
None - Class in org.anchoranalysis.io.output.bean.enabled: No outputs are enabled.
None() - Constructor for class org.anchoranalysis.image.bean.interpolator.None
None() - Constructor for class org.anchoranalysis.io.output.bean.enabled.None
NONE - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
NoneExcept - Class in org.anchoranalysis.io.output.bean.rules: All outputs are disabled except particular ones.
NoneExcept() - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept
NoneExcept(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept: Create with first-level output names
NonEmpty - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a collection must have at least one item.
nonExistingItem(String) - Static method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
nonExistingItem(String, String) - Static method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
NonMaximaSuppression<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce: A strategy for reducing elements that greedily removes any element with a strong overlap with another.
NonMaximaSuppression() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
NonNegative - Annotation Type in org.anchoranalysis.bean.annotation: The bean-field should have a value >= 0
noOverlapWith(Mark, int) - Method in interface org.anchoranalysis.mpp.mark.QuickOverlapCalculation: A quick (computationally-efficient) test to see if we can reject the possibility of overlap
noPadding() - Method in class org.anchoranalysis.image.bean.spatial.Padding
normalisedRadii(Ellipsoid, Optional<Resolution>) - Static method in class org.anchoranalysis.mpp.mark.conic.EllipsoidUtilities
normalize() - Method in class org.anchoranalysis.spatial.point.Vector3d
NormalizeByConstant - Class in org.anchoranalysis.plugin.image.feature.bean.score
NormalizeByConstant() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
NormalizeByMax - Class in org.anchoranalysis.plugin.image.feature.bean.score: This assumes the histograms correspond to the energy channels exactly (in terms of indexing)
NormalizeByMax() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
NormalizeDifferenceToMedian - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Corrects a channel in the following way
NormalizeDifferenceToMedian() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
NormalizedPath - Class in org.anchoranalysis.plugin.io.bean.descriptivename: Uses the normalized path (always with forward slashes) of each file as it's descriptive-name
NormalizedPath() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.NormalizedPath
NormalizedRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range.feature: The range of two feature values (i.e.
NormalizedRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.feature.NormalizedRange
NormalizeObjectIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
NormalizeObjectIntensity() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeObjectIntensity
NoSharedState - Class in org.anchoranalysis.experiment.task: Fake shared-state to use to indicate none exists (for type safety)
Not - Class in org.anchoranalysis.plugin.mpp.bean.check
Not() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.Not
NotFound<T> - Class in org.anchoranalysis.annotation.io.image.findable: A negative-result when an object is NOT found at a particular location.
NotFound(Path, String) - Constructor for class org.anchoranalysis.annotation.io.image.findable.NotFound
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.buffer.PredicateBufferBinary: Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinary: Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryMixed: Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryWithoutOffset: Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferTernary: Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferUnary: Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint: Notifies the processor that there has been a change in z-coordinate
notifyChangeY(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint: Notifies the processor that there has been a change in y-coordinate
notifyChangeZ(int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Notifies the processor that there has been a change in z-coordinate
notifyChangeZ(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: Notifies the processor that there has been a change in z-coordinate
notifyChangeZ(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
notifyChangeZ(int, int, UnsignedByteBuffer) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: Notifies the processor that there has been a change in z-coordinate
notifyChangeZ(int, int, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3NeighborMatchValue
NoTimeSeries - Class in org.anchoranalysis.io.imagej.bean.stack.writer: Base class for ImageJRasterWriter that doesn't support writing time-series as a stack.
NoTimeSeries() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.NoTimeSeries
NotInContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Filters objects to keep only those which are NOT in the container.
NotInContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.NotInContainer
NotTouchingSceneBorder - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Keeps only objects that are not adjacent to the scene-border (i.e.
NotTouchingSceneBorder() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
NullInitParams - Class in org.anchoranalysis.bean.initializable.params
NullMessageLogger - Class in org.anchoranalysis.core.log: Does nothing with (i.e.
NullMessageLogger() - Constructor for class org.anchoranalysis.core.log.NullMessageLogger
NullParamsBean<T> - Class in org.anchoranalysis.bean: A base class for beans that require initialization but the initializations needs no parameters.
NullParamsBean() - Constructor for class org.anchoranalysis.bean.NullParamsBean
NullReporter<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter: Dummy reporter that takes no action.
NullReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
NUMBER_DIGITS_IN_OUTPUT - Static variable in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
NUMBER_ELEMENTS_WRITTEN_ERRORED - Static variable in class org.anchoranalysis.io.output.writer.WriterRouterErrors
NUMBER_ELEMENTS_WRITTEN_NOT_ALLOWED - Static variable in class org.anchoranalysis.io.output.writer.CheckIfAllowed
numberBits() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: The number of bits required to represent a voxel.
numberBorderPixels(ObjectMask, OutlineKernelParameters) - Static method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
numberChannels() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster: A list of channel-names or null if they are not available.
numberChannels() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
NumberChannels - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
NumberChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
numberCompletedFailed() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
numberCompletedFailureJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
numberCompletedJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
numberCompletedSuccess() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
numberCompletedSuccessfullyJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.Orientation
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.Mark
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.PointList
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle2D
numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle3D
numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAxisAngle
numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory: The dimensionality of the rotation-matrix.
numberDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Number of output-names that were not enabled.
NumberDistinctValues - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
NumberDistinctValues() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.NumberDistinctValues
numberEdges() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The number of edges in the graph.
numberEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Number of output-names that were enabled.
numberExecutingJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
numberFoundFrom(Set<Contour>) - Method in class org.anchoranalysis.plugin.points.contour.ContourList
numberFrames() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
numberFrames() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
numberFrames() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
numberFrames() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
numberGPUs() - Method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
numberImageFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
NumberIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
NumberIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjects
NumberIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting: 1.
NumberIntersectingObjectsAboveThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjectsAboveThreshold
numberItemsCurrentlyStored() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap: Number of items currently stored in cache
NumberIterations - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
NumberIterations() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
NumberIterations(int) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
numberManifests() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
NumberMarks - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
NumberMarks - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
NumberMarks() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.collection.NumberMarks
NumberMarks() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.NumberMarks
NumberMarksFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
NumberMarksFromManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
numberMatches() - Method in class org.anchoranalysis.image.core.object.MatchedObject
NumberNeighboringVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy: Calculates the number of voxels on the object that have a neighbor (according to a binary-mask on an energy-channel)
NumberNeighboringVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
numberNonNullConverters() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
numberNotCompleted() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: Number of jobs that have not been completed.
NumberObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.collection
NumberObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.collection.NumberObjects
numberOngoingJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
numberPaired() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
numberPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
numberPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
numberPairFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
NumberPoints - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
NumberPoints() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.NumberPoints
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
numberRegions() - Method in class org.anchoranalysis.mpp.mark.Mark
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.PointList
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
NumberRemovedVoxelsAfterClosing - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological: How many pixels are removed after a morphological closing operation on the object-mask.
NumberRemovedVoxelsAfterClosing() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
numberSeries() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
numberSeries() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
numberSingleFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
numberSlicesProcessed() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
numberTotalScheduledJobs() - Method in class org.anchoranalysis.experiment.task.TaskStatistics: Total number of scheduled jobs.
numberUnassigned(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
numberUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
numberUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
numberUniqueColors() - Method in interface org.anchoranalysis.core.color.ColorIndex
numberUniqueColors() - Method in class org.anchoranalysis.core.color.ColorIndexModulo
numberUniqueColors() - Method in class org.anchoranalysis.core.color.ColorList
numberUniqueColors() - Method in class org.anchoranalysis.core.color.SingleColor
numberVertices() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The number of vertices in the graph.
numberVoxels() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
NumberVoxels - Class in org.anchoranalysis.image.feature.bean.object.single
NumberVoxels() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
NumberVoxelsAtBorder - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
NumberVoxelsAtBorder() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
numberVoxelsOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The number of "ON" voxels on the object-mask
numFrames() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
numGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
numImagesAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
numImagesTotal() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
numImagesWithAcceptedAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
numImagesWithoutAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
numImagesWithSkippedAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
numProbMap() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
numRegions() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
numSlices() - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
numSlices() - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
numSlices() - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
numSlices() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
NumTouchingVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A scheme for counting the touching voxels by intersection of object-masks
NumTouchingVoxelFaces() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxelFaces
NumTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: A scheme for counting touching voxels.
NumTouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxels
numUnassignedLeft() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
numUnassignedRight() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs

O

ObjectAggregationBase<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates a feature for a set of objects using this stack as a energy-stack, and aggregates.
ObjectAggregationBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
ObjectAsPoints - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
ObjectAsPoints() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
ObjectCollection - Class in org.anchoranalysis.image.voxel.object: A collection of ObjectMask
ObjectCollection() - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollection: Creates with no objects
ObjectCollection(Stream<ObjectMask>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollection: Creates with elements from a stream
ObjectCollectionFactory - Class in org.anchoranalysis.image.voxel.object.factory: Creates ObjectCollection using various utility and helper methods
ObjectCollectionProvider - Class in org.anchoranalysis.image.bean.provider
ObjectCollectionProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ObjectCollectionProvider
ObjectCollectionProviderFilterBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
ObjectCollectionProviderFilterBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
ObjectCollectionProviderMorphological - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
ObjectCollectionProviderMorphological() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
ObjectCollectionProviderUnary - Class in org.anchoranalysis.image.bean.provider: Base class for ObjectCollectionProvider that take a objects bean-field of same type as provided.
ObjectCollectionProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
ObjectCollectionProviderWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
ObjectCollectionProviderWithFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
ObjectCollectionRTree - Class in org.anchoranalysis.image.voxel.object: An R-Tree of object-masks (indexed via a derived bounding-box).
ObjectCollectionRTree(ObjectCollection) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree: Creates an r-tree for particular objects.
ObjectCollectionWithProperties - Class in org.anchoranalysis.image.core.object.properties: Like an ObjectCollection but each object has associated properties.
ObjectCollectionWithProperties() - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
ObjectCollectionWithProperties(Stream<ObjectWithProperties>) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
ObjectCollectionWithProperties(ObjectCollection) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
ObjectCollectionWithProperties(ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
ObjectCollectionWithPropertiesFactory - Class in org.anchoranalysis.image.core.object.properties
ObjectComparer - Class in org.anchoranalysis.plugin.annotation.bean.comparer: An object-collection to be used to compare against something
ObjectComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.Base
objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Copies an area corresponding to an object-mask to another Voxels
ObjectDrawAttributes - Class in org.anchoranalysis.overlay.writer: A means of extracting attributes associated with a particular object (e.g.
ObjectDrawAttributes(ColorIndex) - Constructor for class org.anchoranalysis.overlay.writer.ObjectDrawAttributes: Creates with a specific color-index and uses the iteration-index as both the ID and color-ID
ObjectDrawAttributes(ColorIndex, IdentifierGetter<ObjectWithProperties>, IdentifierGetter<ObjectWithProperties>) - Constructor for class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
ObjectDrawAttributesFactory - Class in org.anchoranalysis.overlay.writer
ObjectFilter - Class in org.anchoranalysis.image.bean.object
ObjectFilter() - Constructor for class org.anchoranalysis.image.bean.object.ObjectFilter
ObjectFilterCombine - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: A filter that combines other filters (in a list)
ObjectFilterCombine() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine
ObjectFilterPredicate - Class in org.anchoranalysis.plugin.image.bean.object.filter: Uses a predicate to make a decision whether to keep objects or not.
ObjectFilterPredicate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
ObjectFilterRelation - Class in org.anchoranalysis.plugin.image.bean.object.filter: An independent object-filter that uses a relation in its predicate.
ObjectFilterRelation() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
objectFor(T) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask: An object-mask for a given element.
ObjectInputStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize
ObjectInputStreamDeserializer() - Constructor for class org.anchoranalysis.core.serialize.ObjectInputStreamDeserializer
ObjectIntersectionRemover - Class in org.anchoranalysis.plugin.image.object
ObjectMask - Class in org.anchoranalysis.image.voxel.object: An object expressed in voxels, bounded within overall space.
ObjectMask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
ObjectMask(BoundedVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates an object-mask to correspond to bounded-voxels.
ObjectMask(BoundedVoxels<UnsignedByteBuffer>, BinaryValues) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
ObjectMask(Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates an object-mask with a corner at the origin (i.e.
ObjectMask(BoundingBox) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates an object-mask to corresponding to a bounding-box with all pixels off (0)
ObjectMask(BoundingBox, BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValues) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
ObjectMaskMerger - Class in org.anchoranalysis.image.core.merge: Merges one or more ObjectMasks into a single object
ObjectMaskStream - Class in org.anchoranalysis.image.voxel.object: A custom "stream" like class for various functional-programming operations on ObjectCollection
ObjectMaskStream(ObjectCollection) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMaskStream
ObjectMatcher - Class in org.anchoranalysis.image.bean.object: Matches an object with other objects.
ObjectMatcher() - Constructor for class org.anchoranalysis.image.bean.object.ObjectMatcher
ObjectOutputStreamGenerator<T extends Serializable> - Class in org.anchoranalysis.io.generator.serialized
ObjectOutputStreamGenerator() - Constructor for class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
ObjectOutputStreamGenerator(Optional<String>) - Constructor for class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
ObjectRadiusStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
ObjectRadiusStandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
objects() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
objects() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree: All objects stored in the r-tree (whose order corresponds to indices in delegate
objects() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
objects(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
OBJECTS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories: Where collections of objects are typically placed in a define-experiment output
objectsAreAllInside(Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
ObjectSerializerPeriodicReporter<T extends Serializable> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
ObjectSerializerPeriodicReporter(String) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
objectsForThumbnail(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
objectsForThumbnail(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
objectsForThumbnail(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Selects objects from an input that will be used for thumbnail generation
ObjectsFromConnectedComponentsFactory - Class in org.anchoranalysis.image.voxel.object.factory: Creates a ObjectCollection from the connected-components of a mask or binary-voxels.
ObjectsFromConnectedComponentsFactory() - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
ObjectsFromConnectedComponentsFactory(boolean) - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
ObjectsFromConnectedComponentsFactory(boolean, int) - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
ObjectsFromConnectedComponentsFactory(int) - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
objectsFromOverlays(OverlayCollection) - Static method in class org.anchoranalysis.overlay.collection.OverlayCollectionObjectFactory: Creates objects from whatever Overlays are found in the collection *
ObjectsToCompare - Class in org.anchoranalysis.plugin.annotation.comparison
ObjectsToCompare(ObjectCollection, ObjectCollection) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator: The objects to draw (without any colors) on the background
objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
ObjectVertex - Class in org.anchoranalysis.plugin.image.object.merge: A vertex in a merge graph representing an object (and and an associated payload)
ObjectVertex(ObjectMask, double) - Constructor for class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
ObjectWithEllipse - Class in org.anchoranalysis.plugin.points.calculate.ellipse
ObjectWithEllipse(ObjectMask, Ellipse) - Constructor for class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
ObjectWithMaximumFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Finds the object with the maximum feature-value from a collection.
ObjectWithMaximumFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeature
ObjectWithMaximumFeatureFromEachMatchedCollection - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Finds the object with the maximum feature among a group of matches for each object.
ObjectWithMaximumFeatureFromEachMatchedCollection() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
ObjectWithProperties - Class in org.anchoranalysis.image.core.object.properties: An ObjectMask with associated key-value properties.
ObjectWithProperties(ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
ObjectWithProperties(ObjectMask, Map<String, Object>) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
ObjectWithProperties(BoundingBox) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
obtain(int, AggregateReceiver<T>, PeriodTriggerBank<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
obtain(int, PeriodReceiver<S>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
of(boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborhoodFactory: Gets an appropriate neighborhood
of(boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.SelectDimensionsFactory
of(boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.SelectDimensionsFactory
of(Collection<ObjectMask>...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection with elements copied from existing collections
of(Optional<ObjectCollection>...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection with elements copied from existing collections (if they exist)
of(Stream<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList: Creates a list from a stream.
of(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
of(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
of(CalculationResolver<FeatureInputSingleObject>, MorphologicalIterations, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
of(SessionInput<FeatureInputSingleObject>, boolean) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
of(BinaryVoxels<UnsignedByteBuffer>...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection with elements from the parameter-list of BinaryVoxels converting the voxels in their entireity to an object-mask at the origin.
of(ObjectCollection...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection with elements copied from existing collections
of(ObjectMask...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory: Creates a new collection with elements from the parameter-list
offset(int, int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
offset(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
offset(int, int) - Method in class org.anchoranalysis.spatial.Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent
offset(int, int, int) - Method in class org.anchoranalysis.spatial.Extent: Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent
offset(Point2i) - Method in class org.anchoranalysis.spatial.Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent
offset(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
offset(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent: Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent
offsetGlobal(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
offsetRelative(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
offsetSlice(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
offsetSlice(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent
OffsettedPointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer: Like a PointTwoDimensionalConsumer but also has a buffer offset.
OffsettedScalarTwoDimensionalConsumer<E extends Exception> - Interface in org.anchoranalysis.spatial.point.consumer: Like a ScalarTwoDimensionalConsumer but accepts two coordinates of a point and an offset value.
ofResolved(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
OMETiff - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats: Writes a stack to the filesystem as a OME-XML using the Bioformats library.
OMETiff() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMETiff
OMEXML - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats: Writes a stack to the filesystem as a OME-XML using the Bioformats library.
OMEXML() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMEXML
One - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects one specific channel from a set of stacks
One() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
oneOnly(String, String, boolean, boolean) - Static method in class org.anchoranalysis.bean.initializable.CheckMisconfigured: Checks that one of two properties is defined, but not both simultaneously (exclusive OR).
OneStageGenerator<T> - Class in org.anchoranalysis.io.generator
OneStageGenerator() - Constructor for class org.anchoranalysis.io.generator.OneStageGenerator
ongoingTasksLessThan(int) - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
onInit() - Method in class org.anchoranalysis.bean.NullParamsBean: As there's no parameters we expose a different method
onInit() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
onInit(NullInitParams) - Method in class org.anchoranalysis.bean.NullParamsBean
onInit(KeyValueParamsInitParams) - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
onInit(FeatureInitParams) - Method in class org.anchoranalysis.feature.bean.Feature: Called after initialization.
onInit(SharedFeaturesInitParams) - Method in class org.anchoranalysis.feature.bean.list.ReferencedFeatures
onInit(SharedFeaturesInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
onInit(ImageInitParams) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
onInit(PointsInitParams) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
onInit(P) - Method in class org.anchoranalysis.bean.initializable.InitializableBean: Called after initialization.
OnlyIf - Class in org.anchoranalysis.experiment.bean.log: Logs messages to a particular location ONLY if certain conditions are fulfilled.
OnlyIf() - Constructor for class org.anchoranalysis.experiment.bean.log.OnlyIf
open() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
open() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
open() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
open() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
open() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
open(int, ProgressReporter) - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
open(int, ProgressReporter) - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
OpenCVWriter - Class in org.anchoranalysis.plugin.opencv.bean.writer: Writes a stack to the filesystem using OpenCV and a specified extension.
OpenCVWriter() - Constructor for class org.anchoranalysis.plugin.opencv.bean.writer.OpenCVWriter
openFile(Path) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
openMarksFromFilePath(Path) - Static method in class org.anchoranalysis.test.experiment.TestLoaderMPP
openMarksFromTestPath(String) - Method in class org.anchoranalysis.test.experiment.TestLoaderMPP
openXmlAbsoluteFilePath(String) - Static method in class org.anchoranalysis.test.TestLoader: Opens a XML document - with an absolute path on the filesystem
openXmlAbsoluteFilePath(Path) - Static method in class org.anchoranalysis.test.TestLoader: Opens a XML document - with an absolute path on the filesystem
openXmlFromTestPath(String) - Method in class org.anchoranalysis.test.TestLoader: Opens a XML document - with a path relative to the test root
OperationFailedException - Exception in org.anchoranalysis.core.exception
OperationFailedException(String) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedException
OperationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedException
OperationFailedException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedException
OperationFailedRuntimeException - Exception in org.anchoranalysis.core.exception
OperationFailedRuntimeException(Exception) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedRuntimeException
OperationFailedRuntimeException(String) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedRuntimeException
OperationMap<T> - Class in org.anchoranalysis.mpp.io.input: Stores objects as operations
OperationMap() - Constructor for class org.anchoranalysis.mpp.io.input.OperationMap
OptimizationContext - Class in org.anchoranalysis.mpp.segment.optimization
OptimizationContext(String, EnergySchemeWithSharedFeatures, DualStack, TriggerTerminationCondition, InputOutputContext, RandomNumberGenerator, MarkWithIdentifierFactory) - Constructor for class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
OptimizationScheme<S,U> - Class in org.anchoranalysis.mpp.segment.bean.optimization: An optimization-scheme that uses kernels to make changes to state
OptimizationScheme() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.OptimizationScheme
OptimizationStep<S,T> - Class in org.anchoranalysis.mpp.segment.optimization.step
OptimizationStep() - Constructor for class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
OptimizationStepLogReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
OptimizationStepLogReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
OptimizationTerminatedEarlyException - Exception in org.anchoranalysis.mpp.segment.optimization
OptimizationTerminatedEarlyException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.OptimizationTerminatedEarlyException
OptionalBean - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a field of a class can be set to null (omitted), otherwise by default a bean must always have a non-null value.
OptionalFactory - Class in org.anchoranalysis.bean: Utility functions to create Optional from nullable providers or boolean flags.
OptionalNameValue<V> - Class in org.anchoranalysis.io.generator.combined: A simple container expressing a value and an associationed optional name.
OptionalNameValue(Optional<String>, V) - Constructor for class org.anchoranalysis.io.generator.combined.OptionalNameValue
OptionalOperationUnsupportedException - Exception in org.anchoranalysis.core.exception
OptionalOperationUnsupportedException() - Constructor for exception org.anchoranalysis.core.exception.OptionalOperationUnsupportedException
OptionalOperationUnsupportedException(Exception) - Constructor for exception org.anchoranalysis.core.exception.OptionalOperationUnsupportedException
OptionalOperationUnsupportedException(String) - Constructor for exception org.anchoranalysis.core.exception.OptionalOperationUnsupportedException
OptionalPointProposer - Interface in org.anchoranalysis.mpp.proposer
OptionalUtilities - Class in org.anchoranalysis.core.functional: Additional utility functions for Optional and exceptions.
Or - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation or voxelwise on both masks, modifying {mask} with the result.
Or - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: Applies multiples filter with logical OR i.e.
Or() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Or
Or() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.Or
order(String) - Method in interface org.anchoranalysis.core.index.bounded.OrderProvider
OrderedFeatureList<T extends FeatureInput> - Interface in org.anchoranalysis.mpp.feature.addcriteria
OrderedList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
OrderedList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrderedList
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
orderedListOfFeatures() - Method in interface org.anchoranalysis.mpp.feature.addcriteria.OrderedFeatureList: A list of features used to determine the add-criteria, or null if irrelevant.
orderedListOfFeatures() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
orderedListOfFeatures() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
OrderedRadius - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
OrderedRadius() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
OrderProvider - Interface in org.anchoranalysis.core.index.bounded
orElseGet(Optional<T>, CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: Like Optional.orElseGet(java.util.function.Supplier<? extends T>) but tolerates an exception in the supplier function, which is immediately thrown.
orFlat(Optional<T>...) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities: The first optional if it's present, or the second, or the third etc.
org.anchoranalysis.annotation - package org.anchoranalysis.annotation: Ground truth for an image in diverse forms.
org.anchoranalysis.annotation.image - package org.anchoranalysis.annotation.image: Annotations that apply to an image as a whole.
org.anchoranalysis.annotation.io - package org.anchoranalysis.annotation.io: Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.assignment - package org.anchoranalysis.annotation.io.assignment: A pairing of objects from two collections (bipartite matching).
org.anchoranalysis.annotation.io.assignment.generator - package org.anchoranalysis.annotation.io.assignment.generator: Generates output images to illustrate a Assignment between annotations.
org.anchoranalysis.annotation.io.bean - package org.anchoranalysis.annotation.io.bean: Beans related to reading / writing / specifying annotations.
org.anchoranalysis.annotation.io.bean.comparer - package org.anchoranalysis.annotation.io.bean.comparer: What to compare an annotation (ground truth) against?
org.anchoranalysis.annotation.io.image - package org.anchoranalysis.annotation.io.image: Reading and writing whole-image label annotations.
org.anchoranalysis.annotation.io.image.findable - package org.anchoranalysis.annotation.io.image.findable: The outcome of searching for annotations or images on the file-system.
org.anchoranalysis.annotation.io.mark - package org.anchoranalysis.annotation.io.mark: Reading and writing annotations basedupon marks to the file-system.
org.anchoranalysis.annotation.mark - package org.anchoranalysis.annotation.mark: Annotations that use one or more marks to describe entities in an image.
org.anchoranalysis.bean - package org.anchoranalysis.bean: Defining, loading, initializing Anchor Beans.
org.anchoranalysis.bean.annotation - package org.anchoranalysis.bean.annotation: Annotations that decorate fields in an Anchor Bean.
org.anchoranalysis.bean.define - package org.anchoranalysis.bean.define: Define and related-classes.
org.anchoranalysis.bean.define.adder - package org.anchoranalysis.bean.define.adder: DefineAdder and related-classes.
org.anchoranalysis.bean.error - package org.anchoranalysis.bean.error: Exceptions that can occur executing generic operations on Anchor Beans.
org.anchoranalysis.bean.initializable - package org.anchoranalysis.bean.initializable: Initializing beans with particular parameters, including recursively.
org.anchoranalysis.bean.initializable.params - package org.anchoranalysis.bean.initializable.params: Some kinds of parameters used when initializing beans.
org.anchoranalysis.bean.initializable.property - package org.anchoranalysis.bean.initializable.property: Performing initializion on particular properties in a bean.
org.anchoranalysis.bean.permute - package org.anchoranalysis.bean.permute: Applying permutations to a bean's fields.
org.anchoranalysis.bean.permute.property - package org.anchoranalysis.bean.permute.property: Applying permutations to the properties of a bean.
org.anchoranalysis.bean.permute.setter - package org.anchoranalysis.bean.permute.setter: Setter used to impose a permutation on bean properties.
org.anchoranalysis.bean.provider - package org.anchoranalysis.bean.provider: A means of creating / loading / referencing a bean from another bean or class.
org.anchoranalysis.bean.shared - package org.anchoranalysis.bean.shared: Utility beans which have a generally broader use than a specific module.
org.anchoranalysis.bean.shared.color - package org.anchoranalysis.bean.shared.color: Beans that specify colors.
org.anchoranalysis.bean.shared.color.scheme - package org.anchoranalysis.bean.shared.color.scheme: Beans that create lists or indices of colors according to particular schemes.
org.anchoranalysis.bean.shared.params - package org.anchoranalysis.bean.shared.params: Setting, referencing and initializing key-value parameters.
org.anchoranalysis.bean.shared.params.keyvalue - package org.anchoranalysis.bean.shared.params.keyvalue: Referencing a particular KeyValueParams.
org.anchoranalysis.bean.shared.path - package org.anchoranalysis.bean.shared.path: Defines a root path directory on the filesystem whre files are read / written.
org.anchoranalysis.bean.shared.random - package org.anchoranalysis.bean.shared.random: Specifies a particular type of random-number generator.
org.anchoranalysis.bean.shared.regex - package org.anchoranalysis.bean.shared.regex: Specifies regular-expressions.
org.anchoranalysis.bean.shared.relation - package org.anchoranalysis.bean.shared.relation: Specifies a binary relation of some kind between scalars.
org.anchoranalysis.bean.shared.relation.threshold - package org.anchoranalysis.bean.shared.relation.threshold: Specifies a unary relation to a *threshold* value.
org.anchoranalysis.bean.store - package org.anchoranalysis.bean.store: Adding beans to collections.
org.anchoranalysis.bean.xml - package org.anchoranalysis.bean.xml: Reading Beans from XML files.
org.anchoranalysis.bean.xml.error - package org.anchoranalysis.bean.xml.error: Exceptions that can thrown when loading beans from XML.
org.anchoranalysis.bean.xml.factory - package org.anchoranalysis.bean.xml.factory: Custom factories for loading beans in custom ways from XML.
org.anchoranalysis.browser.launcher - package org.anchoranalysis.browser.launcher: Launching the anchor GUI interactive application from command-line.
org.anchoranalysis.core.cache - package org.anchoranalysis.core.cache: Caching (memozing) calls to a method so an operation does not need to be repeated.
org.anchoranalysis.core.color - package org.anchoranalysis.core.color: Specifying particular colors and groups of colors.
org.anchoranalysis.core.concurrency - package org.anchoranalysis.core.concurrency: Specifying how many CPUs and GPUs can be allocated for some purpose.
org.anchoranalysis.core.exception - package org.anchoranalysis.core.exception: Very general exceptions and base classes for exceptions with wide applicability.
org.anchoranalysis.core.exception.combinable - package org.anchoranalysis.core.exception.combinable: Nested exceptions of similar type that can be combined together in a summary.
org.anchoranalysis.core.exception.friendly - package org.anchoranalysis.core.exception.friendly: Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly error descriptions.
org.anchoranalysis.core.functional - package org.anchoranalysis.core.functional: Utilities and interfaces for applying functional-programming.
org.anchoranalysis.core.functional.checked - package org.anchoranalysis.core.functional.checked: Versions of many functional-interfaces in java.util.function that throw checked-exceptions.
org.anchoranalysis.core.graph - package org.anchoranalysis.core.graph: Data-structures for directed and undirected graphs, with or without an edge payload.
org.anchoranalysis.core.identifier.getter - package org.anchoranalysis.core.identifier.getter: Data structures for adding a unique name (a String or integer identifier) to other entities.
org.anchoranalysis.core.identifier.name - package org.anchoranalysis.core.identifier.name: Data structures for name (String) and value associations.
org.anchoranalysis.core.identifier.provider - package org.anchoranalysis.core.identifier.provider: A collection of named-elements, a NamedProvider, and related operations.
org.anchoranalysis.core.identifier.provider.store - package org.anchoranalysis.core.identifier.provider.store: Data structures like NamedProvider with supporting for adding new elements.
org.anchoranalysis.core.index - package org.anchoranalysis.core.index: Classes to support getting/setting/specifying unique-integers (indices) for elements.
org.anchoranalysis.core.index.bounded - package org.anchoranalysis.core.index.bounded: A range of elements with indiced, bounded to lie between particular a minimum and maximum.
org.anchoranalysis.core.index.bounded.bridge - package org.anchoranalysis.core.index.bounded.bridge: Exposes one type as a BoundedIndexContainer of another type.
org.anchoranalysis.core.log - package org.anchoranalysis.core.log: Interfaces to log messages, both information and error messages.
org.anchoranalysis.core.log.error - package org.anchoranalysis.core.log.error: Mechanism for reporting errors (exceptions/throwables) to the user.
org.anchoranalysis.core.progress - package org.anchoranalysis.core.progress: Classes to allow for tracking the progress of a task that can be broken into smaller units, for reporting to the user.
org.anchoranalysis.core.random - package org.anchoranalysis.core.random: Generating random numbers.
org.anchoranalysis.core.serialize - package org.anchoranalysis.core.serialize: Utilities for serializing and deserializing objects.
org.anchoranalysis.core.system - package org.anchoranalysis.core.system: Utilities for interacting with the operating system or computer system generally
org.anchoranalysis.core.system.path - package org.anchoranalysis.core.system.path: Utilities for converting/manipulating file-paths.
org.anchoranalysis.core.value - package org.anchoranalysis.core.value: Encapsulating values or sets of named-values.
org.anchoranalysis.experiment - package org.anchoranalysis.experiment: Classes related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.bean - package org.anchoranalysis.experiment.bean: Beans related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.bean.identifier - package org.anchoranalysis.experiment.bean.identifier: Assigning unique names to experiments.
org.anchoranalysis.experiment.bean.io - package org.anchoranalysis.experiment.bean.io: Generic experiments that handle input and output in structured ways.
org.anchoranalysis.experiment.bean.log - package org.anchoranalysis.experiment.bean.log: Different approaches to where messages on the progress/status of an experiment are logged to.
org.anchoranalysis.experiment.bean.processor - package org.anchoranalysis.experiment.bean.processor: How a task is executed on multiple inputs.
org.anchoranalysis.experiment.bean.require - package org.anchoranalysis.experiment.bean.require: A test whether certain conditions on arguments to experiments are fulfilled.
org.anchoranalysis.experiment.bean.task - package org.anchoranalysis.experiment.bean.task: Defines a task, which is a set of operations run on an input, that may or may not generate an output.
org.anchoranalysis.experiment.io - package org.anchoranalysis.experiment.io: Interfaces for replacing attributes of an experiment: input, output, task etc.
org.anchoranalysis.experiment.log - package org.anchoranalysis.experiment.log: Helpful classes for logging.
org.anchoranalysis.experiment.task - package org.anchoranalysis.experiment.task: Non-bean classes related to a Task.
org.anchoranalysis.experiment.task.processor - package org.anchoranalysis.experiment.task.processor: Non-bean classes related to JobProcessor.
org.anchoranalysis.feature.bean - package org.anchoranalysis.feature.bean: Beans pertaining to feature-calculation.
org.anchoranalysis.feature.bean.list - package org.anchoranalysis.feature.bean.list: A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.bean.operator - package org.anchoranalysis.feature.bean.operator: Features that are sufficiently generic to work on any input-type.
org.anchoranalysis.feature.bean.provider - package org.anchoranalysis.feature.bean.provider: Provider of a single feature.
org.anchoranalysis.feature.bean.results - package org.anchoranalysis.feature.bean.results: Defines base class FeatureResults together with some implementations.
org.anchoranalysis.feature.calculate - package org.anchoranalysis.feature.calculate: Sub-feature units of calculation that can be cached.
org.anchoranalysis.feature.calculate.cache - package org.anchoranalysis.feature.calculate.cache: Classes to cache feature-results or parts of feature-results that occur repeatedly among features or across calculations of the same feature.
org.anchoranalysis.feature.energy - package org.anchoranalysis.feature.energy
org.anchoranalysis.feature.input - package org.anchoranalysis.feature.input
org.anchoranalysis.feature.io.csv - package org.anchoranalysis.feature.io.csv: Writing feature calculation-results in CSV format.
org.anchoranalysis.feature.io.name - package org.anchoranalysis.feature.io.name: Naming items in a weay that breaks down into multiple elements.
org.anchoranalysis.feature.io.results - package org.anchoranalysis.feature.io.results: Writes feature-calculation results in different formats, also grouped results.
org.anchoranalysis.feature.io.results.group - package org.anchoranalysis.feature.io.results.group: Various different outputs that can be written for the a grouped version of the results in ResultsWriter.
org.anchoranalysis.feature.list - package org.anchoranalysis.feature.list
org.anchoranalysis.feature.name - package org.anchoranalysis.feature.name
org.anchoranalysis.feature.results - package org.anchoranalysis.feature.results: Results from one or more feature calculations.
org.anchoranalysis.feature.session - package org.anchoranalysis.feature.session
org.anchoranalysis.feature.session.cache - package org.anchoranalysis.feature.session.cache
org.anchoranalysis.feature.session.cache.creator - package org.anchoranalysis.feature.session.cache.creator
org.anchoranalysis.feature.session.cache.horizontal - package org.anchoranalysis.feature.session.cache.horizontal
org.anchoranalysis.feature.session.calculator - package org.anchoranalysis.feature.session.calculator
org.anchoranalysis.feature.session.calculator.cached - package org.anchoranalysis.feature.session.calculator.cached
org.anchoranalysis.feature.session.strategy.child - package org.anchoranalysis.feature.session.strategy.child
org.anchoranalysis.feature.session.strategy.replace - package org.anchoranalysis.feature.session.strategy.replace
org.anchoranalysis.feature.session.strategy.replace.bind - package org.anchoranalysis.feature.session.strategy.replace.bind
org.anchoranalysis.feature.shared - package org.anchoranalysis.feature.shared: Features shared for referencing among calculations.
org.anchoranalysis.image.bean - package org.anchoranalysis.image.bean: Core (bean) classes for image processing.
org.anchoranalysis.image.bean.channel.converter - package org.anchoranalysis.image.bean.channel.converter: Base classes for comparing a channel to another type.
org.anchoranalysis.image.bean.interpolator - package org.anchoranalysis.image.bean.interpolator: Beans for specifying image interpolators.
org.anchoranalysis.image.bean.nonbean.error - package org.anchoranalysis.image.bean.nonbean.error: Specific exception types that can be thrown in this module.
org.anchoranalysis.image.bean.nonbean.init - package org.anchoranalysis.image.bean.nonbean.init: Initialization of image-related beans.
org.anchoranalysis.image.bean.nonbean.segment - package org.anchoranalysis.image.bean.nonbean.segment: Non-bean classes relating to image-segmentation.
org.anchoranalysis.image.bean.nonbean.spatial.arrange - package org.anchoranalysis.image.bean.nonbean.spatial.arrange: Non-beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.object - package org.anchoranalysis.image.bean.object: Beans pertaining to ObjectMask and their collections.
org.anchoranalysis.image.bean.provider - package org.anchoranalysis.image.bean.provider: Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.provider.stack - package org.anchoranalysis.image.bean.provider.stack: A provider of Stacks.
org.anchoranalysis.image.bean.segment - package org.anchoranalysis.image.bean.segment: Base classes to perform image segmentation, transforming an image into another meaningful entity or entities.
org.anchoranalysis.image.bean.segment.binary - package org.anchoranalysis.image.bean.segment.binary: Base classes to perform binary-segmentation.
org.anchoranalysis.image.bean.segment.object - package org.anchoranalysis.image.bean.segment.object: Base classes to segment a channel into objects.
org.anchoranalysis.image.bean.spatial - package org.anchoranalysis.image.bean.spatial: Beans to define entities or operate that consider Euclidian space.
org.anchoranalysis.image.bean.spatial.arrange - package org.anchoranalysis.image.bean.spatial.arrange: Beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.spatial.direction - package org.anchoranalysis.image.bean.spatial.direction: Beans to specify a direction.
org.anchoranalysis.image.bean.threshold - package org.anchoranalysis.image.bean.threshold: Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.bean.threshold.relation - package org.anchoranalysis.image.bean.threshold.relation: Reusable relations to a threshold.
org.anchoranalysis.image.bean.unitvalue.distance - package org.anchoranalysis.image.bean.unitvalue.distance: Converting quantities of distance between units.
org.anchoranalysis.image.bean.unitvalue.extent - package org.anchoranalysis.image.bean.unitvalue.extent: Converting quantities of extent (area or volume) between units.
org.anchoranalysis.image.bean.unitvalue.extent.area - package org.anchoranalysis.image.bean.unitvalue.extent.area: Converting quantities of area between units.
org.anchoranalysis.image.bean.unitvalue.extent.volume - package org.anchoranalysis.image.bean.unitvalue.extent.volume: Converting quantities of volume between units.
org.anchoranalysis.image.core.channel - package org.anchoranalysis.image.core.channel: The Channel core data-class and related operations and converters.
org.anchoranalysis.image.core.channel.convert - package org.anchoranalysis.image.core.channel.convert: Converts a channel to other data-types.
org.anchoranalysis.image.core.channel.convert.attached - package org.anchoranalysis.image.core.channel.convert.attached: Converts a channel to another data-type based upon another object to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.channel - package org.anchoranalysis.image.core.channel.convert.attached.channel: Converts a channel to another data-type based upon a Channel to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.histogram - package org.anchoranalysis.image.core.channel.convert.attached.histogram: Converts a channel to another data-type based upon a Histogram to which it is attached.
org.anchoranalysis.image.core.channel.factory - package org.anchoranalysis.image.core.channel.factory: Factory classes for creating Channel for various voxel data-types.
org.anchoranalysis.image.core.dimensions - package org.anchoranalysis.image.core.dimensions: Classes to describe the size of images or components of images both in voxels and physically.
org.anchoranalysis.image.core.mask - package org.anchoranalysis.image.core.mask: An image with only two permissible states.
org.anchoranalysis.image.core.mask.combine - package org.anchoranalysis.image.core.mask.combine: Binary operations involving voxelwise combination of Mask.
org.anchoranalysis.image.core.merge - package org.anchoranalysis.image.core.merge: Merges two or more entities.
org.anchoranalysis.image.core.object - package org.anchoranalysis.image.core.object: The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.core.object.factory - package org.anchoranalysis.image.core.object.factory: Utilities to create ObjectMask and ObjectCollection.
org.anchoranalysis.image.core.object.label - package org.anchoranalysis.image.core.object.label: Labelling elements (object-masks or similar) with unique successive integers in a channel.
org.anchoranalysis.image.core.object.properties - package org.anchoranalysis.image.core.object.properties
org.anchoranalysis.image.core.object.scale - package org.anchoranalysis.image.core.object.scale: Scaling object-collections, or lists of elements with object-representations.
org.anchoranalysis.image.core.object.seed - package org.anchoranalysis.image.core.object.seed
org.anchoranalysis.image.core.orientation - package org.anchoranalysis.image.core.orientation: Various methods to specify the orientation (general direction) of an entity.
org.anchoranalysis.image.core.outline - package org.anchoranalysis.image.core.outline: Finds outline voxels i.e.
org.anchoranalysis.image.core.outline.traverser - package org.anchoranalysis.image.core.outline.traverser: Performs a walk on every voxel on the outline of an object-mask.
org.anchoranalysis.image.core.outline.traverser.path - package org.anchoranalysis.image.core.outline.traverser.path
org.anchoranalysis.image.core.outline.traverser.visited - package org.anchoranalysis.image.core.outline.traverser.visited
org.anchoranalysis.image.core.outline.traverser.visited.combine - package org.anchoranalysis.image.core.outline.traverser.visited.combine
org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy - package org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy
org.anchoranalysis.image.core.points - package org.anchoranalysis.image.core.points
org.anchoranalysis.image.core.stack - package org.anchoranalysis.image.core.stack
org.anchoranalysis.image.core.stack.bufferedimage - package org.anchoranalysis.image.core.stack.bufferedimage
org.anchoranalysis.image.core.stack.rgb - package org.anchoranalysis.image.core.stack.rgb
org.anchoranalysis.image.core.stack.wrap - package org.anchoranalysis.image.core.stack.wrap
org.anchoranalysis.image.experiment.bean.task - package org.anchoranalysis.image.experiment.bean.task
org.anchoranalysis.image.experiment.identifiers - package org.anchoranalysis.image.experiment.identifiers
org.anchoranalysis.image.experiment.label - package org.anchoranalysis.image.experiment.label
org.anchoranalysis.image.experiment.seed - package org.anchoranalysis.image.experiment.seed
org.anchoranalysis.image.feature.bean - package org.anchoranalysis.image.feature.bean: Beans pertaining to feature definition and calculation.
org.anchoranalysis.image.feature.bean.evaluator - package org.anchoranalysis.image.feature.bean.evaluator: Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
org.anchoranalysis.image.feature.bean.object.collection - package org.anchoranalysis.image.feature.bean.object.collection
org.anchoranalysis.image.feature.bean.object.pair - package org.anchoranalysis.image.feature.bean.object.pair
org.anchoranalysis.image.feature.bean.object.single - package org.anchoranalysis.image.feature.bean.object.single
org.anchoranalysis.image.feature.bean.physical - package org.anchoranalysis.image.feature.bean.physical
org.anchoranalysis.image.feature.bean.physical.convert - package org.anchoranalysis.image.feature.bean.physical.convert
org.anchoranalysis.image.feature.bean.score - package org.anchoranalysis.image.feature.bean.score
org.anchoranalysis.image.feature.bean.stack - package org.anchoranalysis.image.feature.bean.stack
org.anchoranalysis.image.feature.evaluator - package org.anchoranalysis.image.feature.evaluator
org.anchoranalysis.image.feature.histogram - package org.anchoranalysis.image.feature.histogram
org.anchoranalysis.image.feature.object.calculation - package org.anchoranalysis.image.feature.object.calculation
org.anchoranalysis.image.feature.object.input - package org.anchoranalysis.image.feature.object.input
org.anchoranalysis.image.feature.session - package org.anchoranalysis.image.feature.session
org.anchoranalysis.image.feature.session.merged - package org.anchoranalysis.image.feature.session.merged
org.anchoranalysis.image.feature.stack - package org.anchoranalysis.image.feature.stack
org.anchoranalysis.image.voxel - package org.anchoranalysis.image.voxel: Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.arithmetic - package org.anchoranalysis.image.voxel.arithmetic: Arithmetic operations for Voxels.
org.anchoranalysis.image.voxel.assigner - package org.anchoranalysis.image.voxel.assigner
org.anchoranalysis.image.voxel.binary - package org.anchoranalysis.image.voxel.binary: The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.binary.values - package org.anchoranalysis.image.voxel.binary.values: Defining on and off intensity-values to interpret an image in a binary way.
org.anchoranalysis.image.voxel.buffer - package org.anchoranalysis.image.voxel.buffer
org.anchoranalysis.image.voxel.buffer.max - package org.anchoranalysis.image.voxel.buffer.max
org.anchoranalysis.image.voxel.buffer.mean - package org.anchoranalysis.image.voxel.buffer.mean
org.anchoranalysis.image.voxel.buffer.primitive - package org.anchoranalysis.image.voxel.buffer.primitive: Conversion of both primitive data types and image structures between Anchor's data-structures and other representations.
org.anchoranalysis.image.voxel.convert - package org.anchoranalysis.image.voxel.convert: Converting Voxels to different data-types.
org.anchoranalysis.image.voxel.convert.imglib2 - package org.anchoranalysis.image.voxel.convert.imglib2: Converts anchor data-structures to those used by ImgLib2.
org.anchoranalysis.image.voxel.datatype - package org.anchoranalysis.image.voxel.datatype
org.anchoranalysis.image.voxel.extracter - package org.anchoranalysis.image.voxel.extracter
org.anchoranalysis.image.voxel.extracter.predicate - package org.anchoranalysis.image.voxel.extracter.predicate
org.anchoranalysis.image.voxel.factory - package org.anchoranalysis.image.voxel.factory
org.anchoranalysis.image.voxel.factory.sliceindex - package org.anchoranalysis.image.voxel.factory.sliceindex
org.anchoranalysis.image.voxel.interpolator - package org.anchoranalysis.image.voxel.interpolator: Different interpolator methods to use when scaling voxels.
org.anchoranalysis.image.voxel.iterator - package org.anchoranalysis.image.voxel.iterator: Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.intersecting - package org.anchoranalysis.image.voxel.iterator.intersecting: Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over the intersecting regions of two entities.
org.anchoranalysis.image.voxel.iterator.neighbor - package org.anchoranalysis.image.voxel.iterator.neighbor: Iterating over a point's neighboring voxels.
org.anchoranalysis.image.voxel.iterator.predicate - package org.anchoranalysis.image.voxel.iterator.predicate: Functional-interfaces for processing different combinations of points and buffers that return a boolean.
org.anchoranalysis.image.voxel.iterator.predicate.buffer - package org.anchoranalysis.image.voxel.iterator.predicate.buffer
org.anchoranalysis.image.voxel.iterator.process - package org.anchoranalysis.image.voxel.iterator.process: Functional-interfaces for processing different combinations of points and buffers that do not return a value.
org.anchoranalysis.image.voxel.iterator.process.buffer - package org.anchoranalysis.image.voxel.iterator.process.buffer: Functional-interfaces for processing different combinations of points and raw buffers, but not VoxelBuffer.
org.anchoranalysis.image.voxel.iterator.process.voxelbuffer - package org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Functional-interfaces for processing different combinations of points and VoxelBuffer but not raw buffers.
org.anchoranalysis.image.voxel.kernel - package org.anchoranalysis.image.voxel.kernel
org.anchoranalysis.image.voxel.kernel.count - package org.anchoranalysis.image.voxel.kernel.count
org.anchoranalysis.image.voxel.kernel.density - package org.anchoranalysis.image.voxel.kernel.density
org.anchoranalysis.image.voxel.kernel.dilateerode - package org.anchoranalysis.image.voxel.kernel.dilateerode
org.anchoranalysis.image.voxel.kernel.outline - package org.anchoranalysis.image.voxel.kernel.outline
org.anchoranalysis.image.voxel.neighborhood - package org.anchoranalysis.image.voxel.neighborhood
org.anchoranalysis.image.voxel.object - package org.anchoranalysis.image.voxel.object
org.anchoranalysis.image.voxel.object.factory - package org.anchoranalysis.image.voxel.object.factory
org.anchoranalysis.image.voxel.object.factory.unionfind - package org.anchoranalysis.image.voxel.object.factory.unionfind: Implements a union-find data-structure for connected-components.
org.anchoranalysis.image.voxel.object.morphological - package org.anchoranalysis.image.voxel.object.morphological
org.anchoranalysis.image.voxel.object.morphological.accept - package org.anchoranalysis.image.voxel.object.morphological.accept
org.anchoranalysis.image.voxel.statistics - package org.anchoranalysis.image.voxel.statistics: Statistics about voxel intensities.
org.anchoranalysis.image.voxel.thresholder - package org.anchoranalysis.image.voxel.thresholder: Thresholding operations on voxels.
org.anchoranalysis.io.bioformats - package org.anchoranalysis.io.bioformats: Non-bean classes for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean - package org.anchoranalysis.io.bioformats.bean: Beans for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean.options - package org.anchoranalysis.io.bioformats.bean.options: User-specified options that can modify an opened-raster (e.g.
org.anchoranalysis.io.bioformats.copyconvert - package org.anchoranalysis.io.bioformats.copyconvert: Converts the byte stream opened by Bioformats into channels of particular data-type.
org.anchoranalysis.io.bioformats.copyconvert.tobyte - package org.anchoranalysis.io.bioformats.copyconvert.tobyte: Converts the byte stream opened by Bioformats into channels of ByteBuffer.
org.anchoranalysis.io.bioformats.copyconvert.tofloat - package org.anchoranalysis.io.bioformats.copyconvert.tofloat: Converts the byte stream opened by Bioformats into channels of FloatBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toint - package org.anchoranalysis.io.bioformats.copyconvert.toint: Converts the byte stream opened by Bioformats into channels of IntBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toshort - package org.anchoranalysis.io.bioformats.copyconvert.toshort: Converts the byte stream opened by Bioformats into channels of ShortBuffer.
org.anchoranalysis.io.generator - package org.anchoranalysis.io.generator: Base-classes and utilities for generators, which write different types of objects to the file system.
org.anchoranalysis.io.generator.collection - package org.anchoranalysis.io.generator.collection: Outputting more than one element collectively using a generator.
org.anchoranalysis.io.generator.combined - package org.anchoranalysis.io.generator.combined: Combining multiple generators into one.
org.anchoranalysis.io.generator.sequence - package org.anchoranalysis.io.generator.sequence: Writing a sequence of elements using a generator.
org.anchoranalysis.io.generator.sequence.pattern - package org.anchoranalysis.io.generator.sequence.pattern
org.anchoranalysis.io.generator.serialized - package org.anchoranalysis.io.generator.serialized: Generators for writing serialized objects.
org.anchoranalysis.io.generator.tabular - package org.anchoranalysis.io.generator.tabular: Generators for writing tabular data, including CSV.
org.anchoranalysis.io.generator.text - package org.anchoranalysis.io.generator.text: Generators for writing textual data, including strings.
org.anchoranalysis.io.generator.xml - package org.anchoranalysis.io.generator.xml: Generators for writing XML data.
org.anchoranalysis.io.imagej.bean.stack.writer - package org.anchoranalysis.io.imagej.bean.stack.writer: Raster-writers that use ImageJ to write images to the filesystem.
org.anchoranalysis.io.imagej.convert - package org.anchoranalysis.io.imagej.convert: Converts to and from ImageJ data-structures for images.
org.anchoranalysis.io.manifest - package org.anchoranalysis.io.manifest
org.anchoranalysis.io.manifest.deserializer - package org.anchoranalysis.io.manifest.deserializer: Classes to read manifests from the file-system.
org.anchoranalysis.io.manifest.directory - package org.anchoranalysis.io.manifest.directory: Entities to indicate a directory in the manifest.
org.anchoranalysis.io.manifest.directory.sequenced - package org.anchoranalysis.io.manifest.directory.sequenced: Classes related to a directory that has a particular sequence of outputted filenames.
org.anchoranalysis.io.manifest.file - package org.anchoranalysis.io.manifest.file: Entities to indicate a file and its role in the manifest.
org.anchoranalysis.io.manifest.finder - package org.anchoranalysis.io.manifest.finder: Methods to search through a manifest-file to find outputs matching certain conditions.
org.anchoranalysis.io.manifest.finder.match - package org.anchoranalysis.io.manifest.finder.match: Predicates that are useful for matching against particular type of objects in finders.
org.anchoranalysis.io.manifest.operationrecorder - package org.anchoranalysis.io.manifest.operationrecorder: Makes a record of each file/subdirectory written as output.
org.anchoranalysis.io.manifest.sequencetype - package org.anchoranalysis.io.manifest.sequencetype: Predictable patterns of indexes as used in sets of outputted files.
org.anchoranalysis.io.output.bean - package org.anchoranalysis.io.output.bean: Beans for the framework around writing files to the file-system.
org.anchoranalysis.io.output.bean.enabled - package org.anchoranalysis.io.output.bean.enabled: Beans indicating whether a particular output is enabled or not.
org.anchoranalysis.io.output.bean.path.prefixer - package org.anchoranalysis.io.output.bean.path.prefixer: Beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.bean.rules - package org.anchoranalysis.io.output.bean.rules: Rules for determining if a particular output is enabled or not in a context of a hierarchy.
org.anchoranalysis.io.output.enabled - package org.anchoranalysis.io.output.enabled: Non-beans pertaining to whether a particular output is enabled or not.
org.anchoranalysis.io.output.enabled.multi - package org.anchoranalysis.io.output.enabled.multi: Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
org.anchoranalysis.io.output.enabled.single - package org.anchoranalysis.io.output.enabled.single: Non-beans that pertain to whether a single level has outputs that are enabled or not.
org.anchoranalysis.io.output.error - package org.anchoranalysis.io.output.error: Exceptions that may be thrown when writing files to the file-system.
org.anchoranalysis.io.output.namestyle - package org.anchoranalysis.io.output.namestyle: Methods of naming a file with an index in the file-name.
org.anchoranalysis.io.output.outputter - package org.anchoranalysis.io.output.outputter: Classes for outputting to particular directories.
org.anchoranalysis.io.output.outputter.directory - package org.anchoranalysis.io.output.outputter.directory: BoundDirectory and related classes.
org.anchoranalysis.io.output.path.prefixer - package org.anchoranalysis.io.output.path.prefixer: Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.recorded - package org.anchoranalysis.io.output.recorded: Classes for recording the output-names used as they are written / queried.
org.anchoranalysis.io.output.writer - package org.anchoranalysis.io.output.writer: Allows a generators to write element(s) to the filesystem.
org.anchoranalysis.io.output.xml - package org.anchoranalysis.io.output.xml: Outputting XML to the file-system.
org.anchoranalysis.launcher - package org.anchoranalysis.launcher
org.anchoranalysis.launcher.config - package org.anchoranalysis.launcher.config
org.anchoranalysis.launcher.executor - package org.anchoranalysis.launcher.executor
org.anchoranalysis.launcher.executor.selectparam - package org.anchoranalysis.launcher.executor.selectparam
org.anchoranalysis.launcher.executor.selectparam.experiment - package org.anchoranalysis.launcher.executor.selectparam.experiment
org.anchoranalysis.launcher.executor.selectparam.io - package org.anchoranalysis.launcher.executor.selectparam.io
org.anchoranalysis.launcher.executor.selectparam.path - package org.anchoranalysis.launcher.executor.selectparam.path
org.anchoranalysis.launcher.executor.selectparam.task - package org.anchoranalysis.launcher.executor.selectparam.task
org.anchoranalysis.launcher.options - package org.anchoranalysis.launcher.options: A centralized location for all command-line options used by the launcher.
org.anchoranalysis.launcher.options.outputs - package org.anchoranalysis.launcher.options.outputs: Adding/removing/changing the output(s) from the experiment via command-line-options.
org.anchoranalysis.launcher.parser - package org.anchoranalysis.launcher.parser
org.anchoranalysis.math.arithmetic - package org.anchoranalysis.math.arithmetic: Performing primitive type conversion, counting and summing.
org.anchoranalysis.math.equation - package org.anchoranalysis.math.equation
org.anchoranalysis.math.histogram - package org.anchoranalysis.math.histogram: The Histogram core data class and related operations.
org.anchoranalysis.math.moment - package org.anchoranalysis.math.moment
org.anchoranalysis.math.optimization - package org.anchoranalysis.math.optimization
org.anchoranalysis.math.relation - package org.anchoranalysis.math.relation: Different kinds of binary-relations.
org.anchoranalysis.math.statistics - package org.anchoranalysis.math.statistics
org.anchoranalysis.mpp.bean - package org.anchoranalysis.mpp.bean
org.anchoranalysis.mpp.bean.anneal - package org.anchoranalysis.mpp.bean.anneal
org.anchoranalysis.mpp.bean.bound - package org.anchoranalysis.mpp.bean.bound
org.anchoranalysis.mpp.bean.init - package org.anchoranalysis.mpp.bean.init
org.anchoranalysis.mpp.bean.mark - package org.anchoranalysis.mpp.bean.mark
org.anchoranalysis.mpp.bean.mark.bounds - package org.anchoranalysis.mpp.bean.mark.bounds
org.anchoranalysis.mpp.bean.mark.factory - package org.anchoranalysis.mpp.bean.mark.factory
org.anchoranalysis.mpp.bean.points - package org.anchoranalysis.mpp.bean.points
org.anchoranalysis.mpp.bean.points.fitter - package org.anchoranalysis.mpp.bean.points.fitter
org.anchoranalysis.mpp.bean.points.updatable - package org.anchoranalysis.mpp.bean.points.updatable
org.anchoranalysis.mpp.bean.proposer - package org.anchoranalysis.mpp.bean.proposer
org.anchoranalysis.mpp.bean.proposer.radii - package org.anchoranalysis.mpp.bean.proposer.radii
org.anchoranalysis.mpp.bean.provider - package org.anchoranalysis.mpp.bean.provider
org.anchoranalysis.mpp.bean.regionmap - package org.anchoranalysis.mpp.bean.regionmap
org.anchoranalysis.mpp.bound - package org.anchoranalysis.mpp.bound
org.anchoranalysis.mpp.feature.addcriteria - package org.anchoranalysis.mpp.feature.addcriteria
org.anchoranalysis.mpp.feature.bean.energy.element - package org.anchoranalysis.mpp.feature.bean.energy.element
org.anchoranalysis.mpp.feature.bean.energy.scheme - package org.anchoranalysis.mpp.feature.bean.energy.scheme
org.anchoranalysis.mpp.feature.bean.mark - package org.anchoranalysis.mpp.feature.bean.mark
org.anchoranalysis.mpp.feature.bean.mark.collection - package org.anchoranalysis.mpp.feature.bean.mark.collection
org.anchoranalysis.mpp.feature.energy - package org.anchoranalysis.mpp.feature.energy
org.anchoranalysis.mpp.feature.energy.marks - package org.anchoranalysis.mpp.feature.energy.marks
org.anchoranalysis.mpp.feature.energy.saved - package org.anchoranalysis.mpp.feature.energy.saved
org.anchoranalysis.mpp.feature.energy.scheme - package org.anchoranalysis.mpp.feature.energy.scheme
org.anchoranalysis.mpp.feature.error - package org.anchoranalysis.mpp.feature.error
org.anchoranalysis.mpp.feature.input.memo - package org.anchoranalysis.mpp.feature.input.memo
org.anchoranalysis.mpp.feature.mark - package org.anchoranalysis.mpp.feature.mark
org.anchoranalysis.mpp.io.bean.input - package org.anchoranalysis.mpp.io.bean.input
org.anchoranalysis.mpp.io.bean.report.feature - package org.anchoranalysis.mpp.io.bean.report.feature
org.anchoranalysis.mpp.io.input - package org.anchoranalysis.mpp.io.input
org.anchoranalysis.mpp.io.marks - package org.anchoranalysis.mpp.io.marks
org.anchoranalysis.mpp.io.marks.generator - package org.anchoranalysis.mpp.io.marks.generator
org.anchoranalysis.mpp.io.output - package org.anchoranalysis.mpp.io.output
org.anchoranalysis.mpp.mark - package org.anchoranalysis.mpp.mark
org.anchoranalysis.mpp.mark.conic - package org.anchoranalysis.mpp.mark.conic
org.anchoranalysis.mpp.mark.points - package org.anchoranalysis.mpp.mark.points
org.anchoranalysis.mpp.mark.set - package org.anchoranalysis.mpp.mark.set
org.anchoranalysis.mpp.mark.voxelized - package org.anchoranalysis.mpp.mark.voxelized
org.anchoranalysis.mpp.mark.voxelized.memo - package org.anchoranalysis.mpp.mark.voxelized.memo
org.anchoranalysis.mpp.overlap - package org.anchoranalysis.mpp.overlap
org.anchoranalysis.mpp.overlay - package org.anchoranalysis.mpp.overlay
org.anchoranalysis.mpp.pair - package org.anchoranalysis.mpp.pair
org.anchoranalysis.mpp.points - package org.anchoranalysis.mpp.points
org.anchoranalysis.mpp.probmap - package org.anchoranalysis.mpp.probmap
org.anchoranalysis.mpp.proposer - package org.anchoranalysis.mpp.proposer
org.anchoranalysis.mpp.proposer.error - package org.anchoranalysis.mpp.proposer.error
org.anchoranalysis.mpp.proposer.visualization - package org.anchoranalysis.mpp.proposer.visualization
org.anchoranalysis.mpp.segment.bean - package org.anchoranalysis.mpp.segment.bean: Beans for segmentation algorithms related to marked-point-processes.
org.anchoranalysis.mpp.segment.bean.define - package org.anchoranalysis.mpp.segment.bean.define: DefineOutputter and its sub-classes.
org.anchoranalysis.mpp.segment.bean.kernel - package org.anchoranalysis.mpp.segment.bean.kernel: Base classes for kernels that transition a configuration of marks (a MarkCollection) into an altered version.
org.anchoranalysis.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.mpp.segment.bean.kernel.proposer
org.anchoranalysis.mpp.segment.bean.optimization - package org.anchoranalysis.mpp.segment.bean.optimization
org.anchoranalysis.mpp.segment.bean.optimization.feedback - package org.anchoranalysis.mpp.segment.bean.optimization.feedback
org.anchoranalysis.mpp.segment.bean.optimization.termination - package org.anchoranalysis.mpp.segment.bean.optimization.termination
org.anchoranalysis.mpp.segment.define - package org.anchoranalysis.mpp.segment.define
org.anchoranalysis.mpp.segment.kernel - package org.anchoranalysis.mpp.segment.kernel
org.anchoranalysis.mpp.segment.kernel.proposer - package org.anchoranalysis.mpp.segment.kernel.proposer
org.anchoranalysis.mpp.segment.optimization - package org.anchoranalysis.mpp.segment.optimization
org.anchoranalysis.mpp.segment.optimization.feedback - package org.anchoranalysis.mpp.segment.optimization.feedback
org.anchoranalysis.mpp.segment.optimization.feedback.aggregate - package org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
org.anchoranalysis.mpp.segment.optimization.feedback.period - package org.anchoranalysis.mpp.segment.optimization.feedback.period
org.anchoranalysis.mpp.segment.optimization.step - package org.anchoranalysis.mpp.segment.optimization.step
org.anchoranalysis.mpp.segment.transformer - package org.anchoranalysis.mpp.segment.transformer
org.anchoranalysis.mpp.voxel.partition - package org.anchoranalysis.mpp.voxel.partition
org.anchoranalysis.mpp.voxel.partition.factory - package org.anchoranalysis.mpp.voxel.partition.factory
org.anchoranalysis.overlay - package org.anchoranalysis.overlay
org.anchoranalysis.overlay.bean - package org.anchoranalysis.overlay.bean
org.anchoranalysis.overlay.collection - package org.anchoranalysis.overlay.collection
org.anchoranalysis.overlay.identifier - package org.anchoranalysis.overlay.identifier
org.anchoranalysis.overlay.object - package org.anchoranalysis.overlay.object
org.anchoranalysis.overlay.object.scaled - package org.anchoranalysis.overlay.object.scaled
org.anchoranalysis.overlay.writer - package org.anchoranalysis.overlay.writer
org.anchoranalysis.plot - package org.anchoranalysis.plot: Plotting data on charts.
org.anchoranalysis.plot.bean - package org.anchoranalysis.plot.bean: Beans for plotting.
org.anchoranalysis.plot.bean.colorscheme - package org.anchoranalysis.plot.bean.colorscheme: Color schemes associated with plots.
org.anchoranalysis.plot.index - package org.anchoranalysis.plot.index: Non-bean plot definitions.
org.anchoranalysis.plugin.annotation.bean.aggregate - package org.anchoranalysis.plugin.annotation.bean.aggregate: Beans to combine two or more annotations.
org.anchoranalysis.plugin.annotation.bean.comparer - package org.anchoranalysis.plugin.annotation.bean.comparer: Comparing the similarity of annotations from two images to each other.
org.anchoranalysis.plugin.annotation.bean.comparison - package org.anchoranalysis.plugin.annotation.bean.comparison
org.anchoranalysis.plugin.annotation.bean.comparison.assigner - package org.anchoranalysis.plugin.annotation.bean.comparison.assigner: Pairs annotations from two different sets, creating an assignment of some type.
org.anchoranalysis.plugin.annotation.bean.file - package org.anchoranalysis.plugin.annotation.bean.file: FilesProviders for providing annotations.
org.anchoranalysis.plugin.annotation.bean.label - package org.anchoranalysis.plugin.annotation.bean.label: A label as used for annotating.
org.anchoranalysis.plugin.annotation.bean.strategy - package org.anchoranalysis.plugin.annotation.bean.strategy: Strategies for how to annotate an image, such label per image etc.
org.anchoranalysis.plugin.annotation.comparison - package org.anchoranalysis.plugin.annotation.comparison: Non-bean classes for comparing two sets of annotations.
org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction - package org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction: Morphological grayscale-reconstruction algorithm.
org.anchoranalysis.plugin.fiji.bean.channel.provider - package org.anchoranalysis.plugin.fiji.bean.channel.provider: Implementations of ChannelProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance - package org.anchoranalysis.plugin.fiji.bean.channel.provider.distance: Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.fiji.bean.define - package org.anchoranalysis.plugin.fiji.bean.define: Implementations of DefineAdderBean that use FIJI.
org.anchoranalysis.plugin.fiji.bean.mask.provider - package org.anchoranalysis.plugin.fiji.bean.mask.provider: Implementations of MaskProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.threshold - package org.anchoranalysis.plugin.fiji.bean.threshold: Implementations of Thresholder that use FIJI.
org.anchoranalysis.plugin.image.bean.blur - package org.anchoranalysis.plugin.image.bean.blur
org.anchoranalysis.plugin.image.bean.box - package org.anchoranalysis.plugin.image.bean.box: Beans pertaining to bounding-boxes.
org.anchoranalysis.plugin.image.bean.channel.convert - package org.anchoranalysis.plugin.image.bean.channel.convert
org.anchoranalysis.plugin.image.bean.channel.convert.histogram - package org.anchoranalysis.plugin.image.bean.channel.convert.histogram
org.anchoranalysis.plugin.image.bean.channel.provider - package org.anchoranalysis.plugin.image.bean.channel.provider
org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic - package org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
org.anchoranalysis.plugin.image.bean.channel.provider.assign - package org.anchoranalysis.plugin.image.bean.channel.provider.assign
org.anchoranalysis.plugin.image.bean.channel.provider.convert - package org.anchoranalysis.plugin.image.bean.channel.provider.convert
org.anchoranalysis.plugin.image.bean.channel.provider.gradient - package org.anchoranalysis.plugin.image.bean.channel.provider.gradient
org.anchoranalysis.plugin.image.bean.channel.provider.intensity - package org.anchoranalysis.plugin.image.bean.channel.provider.intensity
org.anchoranalysis.plugin.image.bean.channel.provider.mask - package org.anchoranalysis.plugin.image.bean.channel.provider.mask
org.anchoranalysis.plugin.image.bean.channel.provider.object - package org.anchoranalysis.plugin.image.bean.channel.provider.object
org.anchoranalysis.plugin.image.bean.channel.provider.score - package org.anchoranalysis.plugin.image.bean.channel.provider.score
org.anchoranalysis.plugin.image.bean.channel.provider.slice - package org.anchoranalysis.plugin.image.bean.channel.provider.slice
org.anchoranalysis.plugin.image.bean.color.provider - package org.anchoranalysis.plugin.image.bean.color.provider
org.anchoranalysis.plugin.image.bean.dimensions.provider - package org.anchoranalysis.plugin.image.bean.dimensions.provider
org.anchoranalysis.plugin.image.bean.histogram.provider - package org.anchoranalysis.plugin.image.bean.histogram.provider
org.anchoranalysis.plugin.image.bean.histogram.threshold - package org.anchoranalysis.plugin.image.bean.histogram.threshold
org.anchoranalysis.plugin.image.bean.mask.provider - package org.anchoranalysis.plugin.image.bean.mask.provider
org.anchoranalysis.plugin.image.bean.mask.provider.combine - package org.anchoranalysis.plugin.image.bean.mask.provider.combine
org.anchoranalysis.plugin.image.bean.mask.provider.convert - package org.anchoranalysis.plugin.image.bean.mask.provider.convert
org.anchoranalysis.plugin.image.bean.mask.provider.dimensions - package org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
org.anchoranalysis.plugin.image.bean.mask.provider.morphological - package org.anchoranalysis.plugin.image.bean.mask.provider.morphological
org.anchoranalysis.plugin.image.bean.mask.provider.predicate - package org.anchoranalysis.plugin.image.bean.mask.provider.predicate
org.anchoranalysis.plugin.image.bean.mask.provider.resize - package org.anchoranalysis.plugin.image.bean.mask.provider.resize
org.anchoranalysis.plugin.image.bean.mask.provider.segment - package org.anchoranalysis.plugin.image.bean.mask.provider.segment
org.anchoranalysis.plugin.image.bean.mask.provider.slice - package org.anchoranalysis.plugin.image.bean.mask.provider.slice
org.anchoranalysis.plugin.image.bean.object.filter - package org.anchoranalysis.plugin.image.bean.object.filter
org.anchoranalysis.plugin.image.bean.object.filter.combine - package org.anchoranalysis.plugin.image.bean.object.filter.combine
org.anchoranalysis.plugin.image.bean.object.filter.dependent - package org.anchoranalysis.plugin.image.bean.object.filter.dependent
org.anchoranalysis.plugin.image.bean.object.filter.independent - package org.anchoranalysis.plugin.image.bean.object.filter.independent
org.anchoranalysis.plugin.image.bean.object.match - package org.anchoranalysis.plugin.image.bean.object.match
org.anchoranalysis.plugin.image.bean.object.provider - package org.anchoranalysis.plugin.image.bean.object.provider
org.anchoranalysis.plugin.image.bean.object.provider.connected - package org.anchoranalysis.plugin.image.bean.object.provider.connected
org.anchoranalysis.plugin.image.bean.object.provider.feature - package org.anchoranalysis.plugin.image.bean.object.provider.feature
org.anchoranalysis.plugin.image.bean.object.provider.filter - package org.anchoranalysis.plugin.image.bean.object.provider.filter
org.anchoranalysis.plugin.image.bean.object.provider.mask - package org.anchoranalysis.plugin.image.bean.object.provider.mask
org.anchoranalysis.plugin.image.bean.object.provider.merge - package org.anchoranalysis.plugin.image.bean.object.provider.merge
org.anchoranalysis.plugin.image.bean.object.provider.morphological - package org.anchoranalysis.plugin.image.bean.object.provider.morphological
org.anchoranalysis.plugin.image.bean.object.provider.segment - package org.anchoranalysis.plugin.image.bean.object.provider.segment
org.anchoranalysis.plugin.image.bean.object.provider.slice - package org.anchoranalysis.plugin.image.bean.object.provider.slice
org.anchoranalysis.plugin.image.bean.object.provider.split - package org.anchoranalysis.plugin.image.bean.object.provider.split
org.anchoranalysis.plugin.image.bean.object.segment.channel - package org.anchoranalysis.plugin.image.bean.object.segment.channel
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
org.anchoranalysis.plugin.image.bean.object.segment.reduce - package org.anchoranalysis.plugin.image.bean.object.segment.reduce: Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
org.anchoranalysis.plugin.image.bean.object.segment.stack - package org.anchoranalysis.plugin.image.bean.object.segment.stack: Instance-segmentation of a Stack.
org.anchoranalysis.plugin.image.bean.params - package org.anchoranalysis.plugin.image.bean.params
org.anchoranalysis.plugin.image.bean.scale - package org.anchoranalysis.plugin.image.bean.scale
org.anchoranalysis.plugin.image.bean.segment.binary - package org.anchoranalysis.plugin.image.bean.segment.binary
org.anchoranalysis.plugin.image.bean.stack.provider - package org.anchoranalysis.plugin.image.bean.stack.provider
org.anchoranalysis.plugin.image.bean.stack.provider.color - package org.anchoranalysis.plugin.image.bean.stack.provider.color
org.anchoranalysis.plugin.image.bean.stack.provider.plot - package org.anchoranalysis.plugin.image.bean.stack.provider.plot
org.anchoranalysis.plugin.image.bean.thumbnail.object - package org.anchoranalysis.plugin.image.bean.thumbnail.object
org.anchoranalysis.plugin.image.bean.thumbnail.stack - package org.anchoranalysis.plugin.image.bean.thumbnail.stack
org.anchoranalysis.plugin.image.box - package org.anchoranalysis.plugin.image.box: Non-beans pertaining to bounding-boxes.
org.anchoranalysis.plugin.image.channel - package org.anchoranalysis.plugin.image.channel
org.anchoranalysis.plugin.image.feature.bean.dimensions - package org.anchoranalysis.plugin.image.feature.bean.dimensions
org.anchoranalysis.plugin.image.feature.bean.histogram.statistic - package org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
org.anchoranalysis.plugin.image.feature.bean.histogram.threshold - package org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
org.anchoranalysis.plugin.image.feature.bean.list.pair - package org.anchoranalysis.plugin.image.feature.bean.list.pair
org.anchoranalysis.plugin.image.feature.bean.list.permute - package org.anchoranalysis.plugin.image.feature.bean.list.permute
org.anchoranalysis.plugin.image.feature.bean.morphological - package org.anchoranalysis.plugin.image.feature.bean.morphological
org.anchoranalysis.plugin.image.feature.bean.object.collection - package org.anchoranalysis.plugin.image.feature.bean.object.collection
org.anchoranalysis.plugin.image.feature.bean.object.combine - package org.anchoranalysis.plugin.image.feature.bean.object.combine
org.anchoranalysis.plugin.image.feature.bean.object.pair - package org.anchoranalysis.plugin.image.feature.bean.object.pair
org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap - package org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
org.anchoranalysis.plugin.image.feature.bean.object.pair.touching - package org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
org.anchoranalysis.plugin.image.feature.bean.object.single - package org.anchoranalysis.plugin.image.feature.bean.object.single
org.anchoranalysis.plugin.image.feature.bean.object.single.border - package org.anchoranalysis.plugin.image.feature.bean.object.single.border
org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox - package org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
org.anchoranalysis.plugin.image.feature.bean.object.single.energy - package org.anchoranalysis.plugin.image.feature.bean.object.single.energy
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
org.anchoranalysis.plugin.image.feature.bean.object.single.moments - package org.anchoranalysis.plugin.image.feature.bean.object.single.moments
org.anchoranalysis.plugin.image.feature.bean.object.single.morphological - package org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
org.anchoranalysis.plugin.image.feature.bean.object.single.shape - package org.anchoranalysis.plugin.image.feature.bean.object.single.shape
org.anchoranalysis.plugin.image.feature.bean.object.single.shared - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared
org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
org.anchoranalysis.plugin.image.feature.bean.object.single.slice - package org.anchoranalysis.plugin.image.feature.bean.object.single.slice
org.anchoranalysis.plugin.image.feature.bean.object.single.surface - package org.anchoranalysis.plugin.image.feature.bean.object.single.surface
org.anchoranalysis.plugin.image.feature.bean.physical - package org.anchoranalysis.plugin.image.feature.bean.physical
org.anchoranalysis.plugin.image.feature.bean.score - package org.anchoranalysis.plugin.image.feature.bean.score
org.anchoranalysis.plugin.image.feature.bean.shared - package org.anchoranalysis.plugin.image.feature.bean.shared
org.anchoranalysis.plugin.image.feature.bean.shared.object - package org.anchoranalysis.plugin.image.feature.bean.shared.object
org.anchoranalysis.plugin.image.feature.bean.stack.intensity - package org.anchoranalysis.plugin.image.feature.bean.stack.intensity
org.anchoranalysis.plugin.image.feature.bean.stack.object - package org.anchoranalysis.plugin.image.feature.bean.stack.object
org.anchoranalysis.plugin.image.feature.object - package org.anchoranalysis.plugin.image.feature.object
org.anchoranalysis.plugin.image.feature.object.calculation.delegate - package org.anchoranalysis.plugin.image.feature.object.calculation.delegate
org.anchoranalysis.plugin.image.feature.object.calculation.single - package org.anchoranalysis.plugin.image.feature.object.calculation.single
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological - package org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
org.anchoranalysis.plugin.image.feature.stack.calculation - package org.anchoranalysis.plugin.image.feature.stack.calculation
org.anchoranalysis.plugin.image.intensity - package org.anchoranalysis.plugin.image.intensity
org.anchoranalysis.plugin.image.intensity.level - package org.anchoranalysis.plugin.image.intensity.level
org.anchoranalysis.plugin.image.object - package org.anchoranalysis.plugin.image.object
org.anchoranalysis.plugin.image.object.merge - package org.anchoranalysis.plugin.image.object.merge
org.anchoranalysis.plugin.image.object.merge.condition - package org.anchoranalysis.plugin.image.object.merge.condition
org.anchoranalysis.plugin.image.object.merge.priority - package org.anchoranalysis.plugin.image.object.merge.priority
org.anchoranalysis.plugin.image.provider - package org.anchoranalysis.plugin.image.provider
org.anchoranalysis.plugin.image.segment - package org.anchoranalysis.plugin.image.segment
org.anchoranalysis.plugin.image.segment.thresholder.slice - package org.anchoranalysis.plugin.image.segment.thresholder.slice
org.anchoranalysis.plugin.image.segment.watershed.encoding - package org.anchoranalysis.plugin.image.segment.watershed.encoding
org.anchoranalysis.plugin.image.task.bean.feature - package org.anchoranalysis.plugin.image.task.bean.feature: Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.feature.source - package org.anchoranalysis.plugin.image.task.bean.feature.source: Source of rows in feature-tables with FeatureSource and derived classes.
org.anchoranalysis.plugin.image.task.bean.format - package org.anchoranalysis.plugin.image.task.bean.format: Tasks for converting image-formats.
org.anchoranalysis.plugin.image.task.bean.format.convertstyle - package org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Different approaches for converting sets of channels (RGB, independently etc.) to another image format.
org.anchoranalysis.plugin.image.task.bean.grouped - package org.anchoranalysis.plugin.image.task.bean.grouped: Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
org.anchoranalysis.plugin.image.task.bean.grouped.histogram - package org.anchoranalysis.plugin.image.task.bean.grouped.histogram: Task(s) to export histograms of intensity values.
org.anchoranalysis.plugin.image.task.bean.grouped.raster - package org.anchoranalysis.plugin.image.task.bean.grouped.raster: Task(s) to calculate the mean of channels grouped together.
org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels - package org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selecting a subset of a set of channels.
org.anchoranalysis.plugin.image.task.bean.labeller - package org.anchoranalysis.plugin.image.task.bean.labeller: Associating labels with images.
org.anchoranalysis.plugin.image.task.bean.scale - package org.anchoranalysis.plugin.image.task.bean.scale
org.anchoranalysis.plugin.image.task.bean.segment - package org.anchoranalysis.plugin.image.task.bean.segment: Tasks to segment an image.
org.anchoranalysis.plugin.image.task.bean.slice - package org.anchoranalysis.plugin.image.task.bean.slice: Tasks that process on one or more slices from a z-stack.
org.anchoranalysis.plugin.image.task.channel - package org.anchoranalysis.plugin.image.task.channel: Non-bean classes pertaining to Channels as used in tasks.
org.anchoranalysis.plugin.image.task.feature - package org.anchoranalysis.plugin.image.task.feature: Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.feature.calculator - package org.anchoranalysis.plugin.image.task.feature.calculator: Non-beans for calculating Features.
org.anchoranalysis.plugin.image.task.grouped - package org.anchoranalysis.plugin.image.task.grouped: Non-bean classes about grouping channels or other inputs.
org.anchoranalysis.plugin.image.task.labeller - package org.anchoranalysis.plugin.image.task.labeller: Non-bean classes about labelling images.
org.anchoranalysis.plugin.image.task.segment - package org.anchoranalysis.plugin.image.task.segment: Non-bean classes for image-segmentation.
org.anchoranalysis.plugin.image.task.slice - package org.anchoranalysis.plugin.image.task.slice: Non-bean cleasses pertaining to tasks that process on one or more slices from a z-stack.
org.anchoranalysis.plugin.image.thumbnail - package org.anchoranalysis.plugin.image.thumbnail: Non-bean classes for thumbnail creation.
org.anchoranalysis.plugin.imagej.bean.channel.provider - package org.anchoranalysis.plugin.imagej.bean.channel.provider
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
org.anchoranalysis.plugin.imagej.bean.define - package org.anchoranalysis.plugin.imagej.bean.define
org.anchoranalysis.plugin.imagej.bean.interpolator - package org.anchoranalysis.plugin.imagej.bean.interpolator
org.anchoranalysis.plugin.imagej.bean.mask.provider - package org.anchoranalysis.plugin.imagej.bean.mask.provider
org.anchoranalysis.plugin.imagej.bean.object.provider - package org.anchoranalysis.plugin.imagej.bean.object.provider
org.anchoranalysis.plugin.imagej.bean.object.segment - package org.anchoranalysis.plugin.imagej.bean.object.segment
org.anchoranalysis.plugin.imagej.bean.stack.provider - package org.anchoranalysis.plugin.imagej.bean.stack.provider
org.anchoranalysis.plugin.imagej.bean.threshold - package org.anchoranalysis.plugin.imagej.bean.threshold
org.anchoranalysis.plugin.imagej.channel.provider - package org.anchoranalysis.plugin.imagej.channel.provider
org.anchoranalysis.plugin.imagej.mask - package org.anchoranalysis.plugin.imagej.mask
org.anchoranalysis.plugin.io.bean.channel.map - package org.anchoranalysis.plugin.io.bean.channel.map
org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod - package org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
org.anchoranalysis.plugin.io.bean.copyfilesmode.naming - package org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
org.anchoranalysis.plugin.io.bean.descriptivename - package org.anchoranalysis.plugin.io.bean.descriptivename
org.anchoranalysis.plugin.io.bean.descriptivename.patternspan - package org.anchoranalysis.plugin.io.bean.descriptivename.patternspan
org.anchoranalysis.plugin.io.bean.experiment - package org.anchoranalysis.plugin.io.bean.experiment
org.anchoranalysis.plugin.io.bean.filepath - package org.anchoranalysis.plugin.io.bean.filepath
org.anchoranalysis.plugin.io.bean.filepath.prefixer - package org.anchoranalysis.plugin.io.bean.filepath.prefixer
org.anchoranalysis.plugin.io.bean.groupfiles - package org.anchoranalysis.plugin.io.bean.groupfiles
org.anchoranalysis.plugin.io.bean.groupfiles.check - package org.anchoranalysis.plugin.io.bean.groupfiles.check
org.anchoranalysis.plugin.io.bean.groupfiles.parser - package org.anchoranalysis.plugin.io.bean.groupfiles.parser
org.anchoranalysis.plugin.io.bean.input - package org.anchoranalysis.plugin.io.bean.input
org.anchoranalysis.plugin.io.bean.input.channel - package org.anchoranalysis.plugin.io.bean.input.channel
org.anchoranalysis.plugin.io.bean.input.files - package org.anchoranalysis.plugin.io.bean.input.files
org.anchoranalysis.plugin.io.bean.input.files.provider - package org.anchoranalysis.plugin.io.bean.input.files.provider
org.anchoranalysis.plugin.io.bean.input.filter - package org.anchoranalysis.plugin.io.bean.input.filter
org.anchoranalysis.plugin.io.bean.input.manifest - package org.anchoranalysis.plugin.io.bean.input.manifest
org.anchoranalysis.plugin.io.bean.input.stack - package org.anchoranalysis.plugin.io.bean.input.stack
org.anchoranalysis.plugin.io.bean.path.derive - package org.anchoranalysis.plugin.io.bean.path.derive
org.anchoranalysis.plugin.io.bean.provider.file - package org.anchoranalysis.plugin.io.bean.provider.file
org.anchoranalysis.plugin.io.bean.stack.reader - package org.anchoranalysis.plugin.io.bean.stack.reader
org.anchoranalysis.plugin.io.bean.stack.writer - package org.anchoranalysis.plugin.io.bean.stack.writer
org.anchoranalysis.plugin.io.bean.stack.writer.bioformats - package org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
org.anchoranalysis.plugin.io.bean.summarizer - package org.anchoranalysis.plugin.io.bean.summarizer
org.anchoranalysis.plugin.io.bean.summarizer.image - package org.anchoranalysis.plugin.io.bean.summarizer.image
org.anchoranalysis.plugin.io.bean.summarizer.input - package org.anchoranalysis.plugin.io.bean.summarizer.input
org.anchoranalysis.plugin.io.bean.summarizer.path - package org.anchoranalysis.plugin.io.bean.summarizer.path
org.anchoranalysis.plugin.io.bean.task - package org.anchoranalysis.plugin.io.bean.task
org.anchoranalysis.plugin.io.input.filter - package org.anchoranalysis.plugin.io.input.filter
org.anchoranalysis.plugin.io.input.path - package org.anchoranalysis.plugin.io.input.path
org.anchoranalysis.plugin.io.manifest - package org.anchoranalysis.plugin.io.manifest
org.anchoranalysis.plugin.io.multifile - package org.anchoranalysis.plugin.io.multifile
org.anchoranalysis.plugin.io.multifile.buffer - package org.anchoranalysis.plugin.io.multifile.buffer
org.anchoranalysis.plugin.io.summarizer - package org.anchoranalysis.plugin.io.summarizer
org.anchoranalysis.plugin.io.xml - package org.anchoranalysis.plugin.io.xml: Reading and writing metadata XML.
org.anchoranalysis.plugin.ml.bean.classifier - package org.anchoranalysis.plugin.ml.bean.classifier
org.anchoranalysis.plugin.ml.bean.cluster - package org.anchoranalysis.plugin.ml.bean.cluster: Beans that perform clustering in some way.
org.anchoranalysis.plugin.mpp.bean.addcriteria - package org.anchoranalysis.plugin.mpp.bean.addcriteria
org.anchoranalysis.plugin.mpp.bean.bound - package org.anchoranalysis.plugin.mpp.bean.bound
org.anchoranalysis.plugin.mpp.bean.check - package org.anchoranalysis.plugin.mpp.bean.check
org.anchoranalysis.plugin.mpp.bean.define - package org.anchoranalysis.plugin.mpp.bean.define
org.anchoranalysis.plugin.mpp.bean.distance - package org.anchoranalysis.plugin.mpp.bean.distance
org.anchoranalysis.plugin.mpp.bean.object.provider - package org.anchoranalysis.plugin.mpp.bean.object.provider
org.anchoranalysis.plugin.mpp.bean.outline - package org.anchoranalysis.plugin.mpp.bean.outline
org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler - package org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
org.anchoranalysis.plugin.mpp.bean.proposer.merge - package org.anchoranalysis.plugin.mpp.bean.proposer.merge
org.anchoranalysis.plugin.mpp.bean.proposer.orientation - package org.anchoranalysis.plugin.mpp.bean.proposer.orientation
org.anchoranalysis.plugin.mpp.bean.proposer.points - package org.anchoranalysis.plugin.mpp.bean.proposer.points
org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation - package org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline - package org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline
org.anchoranalysis.plugin.mpp.bean.proposer.position - package org.anchoranalysis.plugin.mpp.bean.proposer.position
org.anchoranalysis.plugin.mpp.bean.proposer.radii - package org.anchoranalysis.plugin.mpp.bean.proposer.radii
org.anchoranalysis.plugin.mpp.bean.proposer.scalar - package org.anchoranalysis.plugin.mpp.bean.proposer.scalar
org.anchoranalysis.plugin.mpp.bean.proposer.split - package org.anchoranalysis.plugin.mpp.bean.proposer.split
org.anchoranalysis.plugin.mpp.bean.provider.collection - package org.anchoranalysis.plugin.mpp.bean.provider.collection
org.anchoranalysis.plugin.mpp.bean.provider.single - package org.anchoranalysis.plugin.mpp.bean.provider.single
org.anchoranalysis.plugin.mpp.bean.region - package org.anchoranalysis.plugin.mpp.bean.region
org.anchoranalysis.plugin.mpp.bean.segment.binary - package org.anchoranalysis.plugin.mpp.bean.segment.binary
org.anchoranalysis.plugin.mpp.bean.stack.provider - package org.anchoranalysis.plugin.mpp.bean.stack.provider
org.anchoranalysis.plugin.mpp.experiment.bean - package org.anchoranalysis.plugin.mpp.experiment.bean
org.anchoranalysis.plugin.mpp.experiment.bean.define - package org.anchoranalysis.plugin.mpp.experiment.bean.define
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
org.anchoranalysis.plugin.mpp.experiment.bean.feature.source - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.source
org.anchoranalysis.plugin.mpp.experiment.bean.objects - package org.anchoranalysis.plugin.mpp.experiment.bean.objects
org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition - package org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
org.anchoranalysis.plugin.mpp.experiment.bean.output - package org.anchoranalysis.plugin.mpp.experiment.bean.output
org.anchoranalysis.plugin.mpp.experiment.bean.segment - package org.anchoranalysis.plugin.mpp.experiment.bean.segment
org.anchoranalysis.plugin.mpp.experiment.objects - package org.anchoranalysis.plugin.mpp.experiment.objects
org.anchoranalysis.plugin.mpp.experiment.objects.csv - package org.anchoranalysis.plugin.mpp.experiment.objects.csv
org.anchoranalysis.plugin.mpp.feature.bean.mark.collection - package org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
org.anchoranalysis.plugin.mpp.feature.bean.mark.direction - package org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
org.anchoranalysis.plugin.mpp.feature.bean.mark.radii - package org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
org.anchoranalysis.plugin.mpp.feature.bean.mark.region - package org.anchoranalysis.plugin.mpp.feature.bean.mark.region
org.anchoranalysis.plugin.mpp.feature.bean.memo.all - package org.anchoranalysis.plugin.mpp.feature.bean.memo.all
org.anchoranalysis.plugin.mpp.feature.bean.memo.ind - package org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
org.anchoranalysis.plugin.mpp.feature.bean.unit - package org.anchoranalysis.plugin.mpp.feature.bean.unit
org.anchoranalysis.plugin.mpp.feature.overlap - package org.anchoranalysis.plugin.mpp.feature.overlap
org.anchoranalysis.plugin.mpp.segment - package org.anchoranalysis.plugin.mpp.segment
org.anchoranalysis.plugin.mpp.segment.bean.annealing - package org.anchoranalysis.plugin.mpp.segment.bean.annealing
org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized
org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
org.anchoranalysis.plugin.mpp.segment.bean.marks - package org.anchoranalysis.plugin.mpp.segment.bean.marks
org.anchoranalysis.plugin.mpp.segment.bean.marks.dual - package org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
org.anchoranalysis.plugin.mpp.segment.bean.marks.partition - package org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized - package org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
org.anchoranalysis.plugin.mpp.segment.bean.marks.weight - package org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
org.anchoranalysis.plugin.mpp.segment.kernel.assigner - package org.anchoranalysis.plugin.mpp.segment.kernel.assigner
org.anchoranalysis.plugin.mpp.segment.kernel.updater - package org.anchoranalysis.plugin.mpp.segment.kernel.updater
org.anchoranalysis.plugin.mpp.segment.optimization - package org.anchoranalysis.plugin.mpp.segment.optimization
org.anchoranalysis.plugin.opencv - package org.anchoranalysis.plugin.opencv
org.anchoranalysis.plugin.opencv.bean.feature - package org.anchoranalysis.plugin.opencv.bean.feature
org.anchoranalysis.plugin.opencv.bean.object.segment.stack - package org.anchoranalysis.plugin.opencv.bean.object.segment.stack
org.anchoranalysis.plugin.opencv.bean.stack.provider.color - package org.anchoranalysis.plugin.opencv.bean.stack.provider.color
org.anchoranalysis.plugin.opencv.bean.writer - package org.anchoranalysis.plugin.opencv.bean.writer: Implementations of StackWriter and any other types of writers that use OpenCV.
org.anchoranalysis.plugin.opencv.convert - package org.anchoranalysis.plugin.opencv.convert
org.anchoranalysis.plugin.operator.feature.bean - package org.anchoranalysis.plugin.operator.feature.bean
org.anchoranalysis.plugin.operator.feature.bean.arithmetic - package org.anchoranalysis.plugin.operator.feature.bean.arithmetic
org.anchoranalysis.plugin.operator.feature.bean.conditional - package org.anchoranalysis.plugin.operator.feature.bean.conditional
org.anchoranalysis.plugin.operator.feature.bean.list - package org.anchoranalysis.plugin.operator.feature.bean.list
org.anchoranalysis.plugin.operator.feature.bean.range - package org.anchoranalysis.plugin.operator.feature.bean.range
org.anchoranalysis.plugin.operator.feature.bean.range.feature - package org.anchoranalysis.plugin.operator.feature.bean.range.feature
org.anchoranalysis.plugin.operator.feature.bean.replace - package org.anchoranalysis.plugin.operator.feature.bean.replace
org.anchoranalysis.plugin.operator.feature.bean.score - package org.anchoranalysis.plugin.operator.feature.bean.score
org.anchoranalysis.plugin.operator.feature.physical - package org.anchoranalysis.plugin.operator.feature.physical
org.anchoranalysis.plugin.operator.feature.score - package org.anchoranalysis.plugin.operator.feature.score
org.anchoranalysis.plugin.points.bean.contour - package org.anchoranalysis.plugin.points.bean.contour
org.anchoranalysis.plugin.points.bean.feature.object.conic - package org.anchoranalysis.plugin.points.bean.feature.object.conic
org.anchoranalysis.plugin.points.bean.fitter - package org.anchoranalysis.plugin.points.bean.fitter
org.anchoranalysis.plugin.points.bean.mark.proposer.single - package org.anchoranalysis.plugin.points.bean.mark.proposer.single
org.anchoranalysis.plugin.points.bean.mark.provider.collection - package org.anchoranalysis.plugin.points.bean.mark.provider.collection
org.anchoranalysis.plugin.points.bean.mark.provider.single - package org.anchoranalysis.plugin.points.bean.mark.provider.single
org.anchoranalysis.plugin.points.bean.mask.provider - package org.anchoranalysis.plugin.points.bean.mask.provider
org.anchoranalysis.plugin.points.bean.provider.object - package org.anchoranalysis.plugin.points.bean.provider.object
org.anchoranalysis.plugin.points.calculate - package org.anchoranalysis.plugin.points.calculate
org.anchoranalysis.plugin.points.calculate.ellipse - package org.anchoranalysis.plugin.points.calculate.ellipse
org.anchoranalysis.plugin.points.calculate.ellipsoid - package org.anchoranalysis.plugin.points.calculate.ellipsoid
org.anchoranalysis.plugin.points.contour - package org.anchoranalysis.plugin.points.contour
org.anchoranalysis.plugin.points.convexhull - package org.anchoranalysis.plugin.points.convexhull
org.anchoranalysis.plugin.quick.bean.experiment - package org.anchoranalysis.plugin.quick.bean.experiment
org.anchoranalysis.plugin.quick.bean.file.path.derive - package org.anchoranalysis.plugin.quick.bean.file.path.derive
org.anchoranalysis.plugin.quick.bean.input - package org.anchoranalysis.plugin.quick.bean.input
org.anchoranalysis.plugin.quick.bean.input.filepathappend - package org.anchoranalysis.plugin.quick.bean.input.filepathappend
org.anchoranalysis.plugin.quick.bean.structure - package org.anchoranalysis.plugin.quick.bean.structure
org.anchoranalysis.spatial - package org.anchoranalysis.spatial
org.anchoranalysis.spatial.axis - package org.anchoranalysis.spatial.axis: Identifying the three standard axes in 3D cartesian coordinates.
org.anchoranalysis.spatial.box - package org.anchoranalysis.spatial.box: Axis-aligned bounding-boxes and related operations.
org.anchoranalysis.spatial.point - package org.anchoranalysis.spatial.point: A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
org.anchoranalysis.spatial.point.consumer - package org.anchoranalysis.spatial.point.consumer: Functional interfaces that accept cartesian coordinate points specified in different ways.
org.anchoranalysis.spatial.rotation - package org.anchoranalysis.spatial.rotation: A matrix to apply a rotation to a point.
org.anchoranalysis.spatial.rotation.factory - package org.anchoranalysis.spatial.rotation.factory: Creates RotationMatrix in varying ways.
org.anchoranalysis.spatial.rtree - package org.anchoranalysis.spatial.rtree: R-Tree data structure and related operations.
org.anchoranalysis.spatial.scale - package org.anchoranalysis.spatial.scale: How to much to scale an entity in Cartesian space by.
org.anchoranalysis.test - package org.anchoranalysis.test: Testing utilities and fixtures with no greater downstream dependency than anchor-core.
org.anchoranalysis.test.experiment - package org.anchoranalysis.test.experiment: Testing utilities and fixtures with no greater downstream dependency than anchor-experiment or anchor-mpp or anchor-mpp-io.
org.anchoranalysis.test.experiment.launcher - package org.anchoranalysis.test.experiment.launcher: Launches an anchor binary from a shell and runs an experiment.
org.anchoranalysis.test.feature - package org.anchoranalysis.test.feature: Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
org.anchoranalysis.test.feature.plugins - package org.anchoranalysis.test.feature.plugins: Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.
org.anchoranalysis.test.feature.plugins.mockfeature - package org.anchoranalysis.test.feature.plugins.mockfeature: A mocked feature internally using a feature-calculation.
org.anchoranalysis.test.feature.plugins.objects - package org.anchoranalysis.test.feature.plugins.objects: Fixtures for creating object-masks and related feature-inputs.
OrientableBounds - Class in org.anchoranalysis.mpp.bean.bound
OrientableBounds() - Constructor for class org.anchoranalysis.mpp.bean.bound.OrientableBounds
Orientation - Class in org.anchoranalysis.image.core.orientation
Orientation() - Constructor for class org.anchoranalysis.image.core.orientation.Orientation
Orientation2D - Class in org.anchoranalysis.image.core.orientation
Orientation2D() - Constructor for class org.anchoranalysis.image.core.orientation.Orientation2D
Orientation2D(double) - Constructor for class org.anchoranalysis.image.core.orientation.Orientation2D
Orientation3DEulerAngles - Class in org.anchoranalysis.image.core.orientation
Orientation3DEulerAngles() - Constructor for class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
Orientation3DEulerAngles(double, double, double) - Constructor for class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
OrientationAndRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single: Proposes both an orientation and radii for a ConicBase
OrientationAndRadiiProposer(RadiiProposer, OrientationProposer) - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
OrientationAxisAngle - Class in org.anchoranalysis.image.core.orientation: An orientation in axis-angle representation.
OrientationAxisAngle(Vector3d, double) - Constructor for class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
OrientationIdentity - Class in org.anchoranalysis.image.core.orientation
OrientationIdentity(int) - Constructor for class org.anchoranalysis.image.core.orientation.OrientationIdentity
OrientationProposer - Class in org.anchoranalysis.mpp.bean.proposer
OrientationProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.OrientationProposer
OrientationRotationMatrix - Class in org.anchoranalysis.image.core.orientation
OrientationRotationMatrix() - Constructor for class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
OrientationRotationMatrix(RotationMatrix) - Constructor for class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
otherVertex(V) - Method in class org.anchoranalysis.core.graph.TypedEdge: The other vertex on the edge
Otsu - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Performs auto-thresholding using Otsu's method.
Otsu() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
OtsuWeighted - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Similar to Otsu, but weighs the variances differently of background and foreground
OtsuWeighted() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
OtsuWeighted(double, double) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: Provides a prefix which can be prepended to all output files.
outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
outFilePrefixAvoidResolve(NamedPath, String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: Provides a prefix which can be prepended to all output files.
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: Determines the out-file prefix from a path
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.FromDescriptiveName
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx
outgoingEdgesFor(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: All outgoing edges for a given vertex.
outline(Mask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.outline.FindOutline: Creates an outline of depth 1 from a mask
outline(ObjectMask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.outline.FindOutline: Creates outline from an object
Outline - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Always creates a new mask for the result (no need to duplicate input)
Outline() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
outlineGuess3D(Mask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.outline.FindOutline: Finds the outline of a mask, guessing whether to do this in 2D or 3D depending on if the mask has 3-dimensions
OutlineKernel3 - Class in org.anchoranalysis.image.voxel.kernel.outline
OutlineKernel3(BinaryValuesByte, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3
OutlineKernel3(BinaryValuesByte, OutlineKernelParameters) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3
OutlineKernel3Base - Class in org.anchoranalysis.image.voxel.kernel.outline
OutlineKernel3Base(BinaryValuesByte, OutlineKernelParameters) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3Base
OutlineKernel3NeighborMatchValue - Class in org.anchoranalysis.image.voxel.kernel.outline
OutlineKernel3NeighborMatchValue(ObjectMask, BinaryVoxels<UnsignedByteBuffer>, OutlineKernelParameters) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3NeighborMatchValue
OutlineKernelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
OutlineKernelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
OutlineKernelParameters - Class in org.anchoranalysis.image.voxel.kernel.outline
OutlineKernelParameters(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
OutlinePixelsRetriever - Class in org.anchoranalysis.plugin.mpp.bean.outline
OutlinePixelsRetriever() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.OutlinePixelsRetriever
OutlinePreserveRelativeSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object: Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it centered in a window of a certain size.
OutlinePreserveRelativeSize() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
OutlineTraverser - Class in org.anchoranalysis.image.core.outline.traverser
OutlineTraverser(ObjectMask, ConsiderVisit, boolean, boolean) - Constructor for class org.anchoranalysis.image.core.outline.traverser.OutlineTraverser
output(String, boolean) - Method in class org.anchoranalysis.io.generator.collection.NamedProviderOutputter: Outputs the entities using a particular output-name.
OUTPUT_DEFAULT_NON_AGGREGATED - Static variable in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames: If not otherwise specified, the output name for a non-aggregated CSV of the results.
OUTPUT_NAME_MANIFEST - Static variable in class org.anchoranalysis.experiment.bean.io.OutputExperiment
OUTPUT_NAME_MANIFEST - Static variable in class org.anchoranalysis.experiment.bean.task.Task
OUTPUT_RESULTS - Static variable in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
OUTPUT_SUMMARY_CSV - Static variable in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
OUTPUT_THUMBNAILS - Static variable in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
outputAfterAllTasksAreExecuted(Outputter) - Method in interface org.anchoranalysis.mpp.segment.bean.ExperimentState
outputAfterAllTasksAreExecuted(Outputter) - Method in class org.anchoranalysis.plugin.mpp.segment.SgmnMPPState
outputBeforeAnyTasksAreExecuted(Outputter) - Method in interface org.anchoranalysis.mpp.segment.bean.ExperimentState
outputBeforeAnyTasksAreExecuted(Outputter) - Method in class org.anchoranalysis.plugin.mpp.segment.SgmnMPPState
OutputDirectoryAlreadyExistsException - Exception in org.anchoranalysis.io.output.error: When an output-directory already exists.
OutputDirectoryAlreadyExistsException(String) - Constructor for exception org.anchoranalysis.io.output.error.OutputDirectoryAlreadyExistsException
OutputEnabled - Class in org.anchoranalysis.io.output.bean.enabled: Whether a particular output, identified by a textual name, is enabled or not.
OutputEnabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.OutputEnabled
OutputEnabledDelta - Class in org.anchoranalysis.io.output.recorded: Additional output-names to enable or disable from an existing set of output-enabled rules.
OutputEnabledDelta() - Constructor for class org.anchoranalysis.io.output.recorded.OutputEnabledDelta
OutputEnabledMutable - Class in org.anchoranalysis.io.output.enabled: A specific set of first-level outputs are enabled, to which more can be added.
OutputEnabledMutable(String...) - Constructor for class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Creates with one or more enabled outputs.
OutputEnabledMutable(SingleLevelOutputEnabled, String...) - Constructor for class org.anchoranalysis.io.output.enabled.OutputEnabledMutable: Creates with one or more enabled outputs.
OutputEnabledRules - Class in org.anchoranalysis.io.output.bean.rules: Bean that specifies an implementation of MultiLevelOutputEnabled.
OutputEnabledRules() - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnabledRules
OutputEnableRulesSpecify - Class in org.anchoranalysis.io.output.bean.rules: Base class for an OutputEnabledRules that specifies particular output-names for first and second levels.
OutputEnableRulesSpecify() - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
OutputEnableRulesSpecify(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Create with a specific set of first-level output names.
OutputExperiment - Class in org.anchoranalysis.experiment.bean.io: An experiment that uses a OutputManager to specify the outputting of results.
OutputExperiment() - Constructor for class org.anchoranalysis.experiment.bean.io.OutputExperiment
OutputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.io: SelectParam<Path> factory for outputs.
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
outputGroupedData(ConsistentChannelChecker, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName: Outputs the "grouped" data to the filesystem
outputHeaderToWriter(PrintWriter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
outputHeaderToWriter(PrintWriter, String) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
OutputManager - Class in org.anchoranalysis.io.output.bean: Responsible for making decisions on where output goes and what form it takes.
OutputManager() - Constructor for class org.anchoranalysis.io.output.bean.OutputManager
outputName(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch: Match a file whose output-name matches a specific value.
outputNames() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata: Names for any outputs produced by ResultsWriter.
OutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
OutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.OutputNameStyle
OutputPattern - Class in org.anchoranalysis.io.generator.sequence.pattern: How the output of the sequence looks on the filesystem and in the manifest.
OutputPattern(Optional<String>, IndexableOutputNameStyle, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
OutputPatternIntegerSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern: A OutputPattern that outputs a file-name with a trailing integer index.
OutputPatternIntegerSuffix(String, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix: Creates in a subdirectory, using the outputName as both the subdirectory name and the prefix.
OutputPatternIntegerSuffix(String, boolean, String, int, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix: Creates with a full set of flexibility about how the filename appears and whether a subdirectory is used.
OutputPatternIntegerSuffix(String, int, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix: Like OutputPatternIntegerSuffix(String, boolean) but with additional options on the manifest-folder description and whether to check outputs against rules.
OutputPatternIntegerSuffix(String, String) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix: Creates in a subdirectory, using the output-name as the subdirectory name, and a specific prefix.
OutputPatternIntegerSuffix(String, String, int, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix: Like OutputPatternIntegerSuffix(String, String) but with additional options about the number of digits, the manifest-folder description and whether to check outputs against rules.
OutputPatternStringSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern: A OutputPattern that outputs a file-name with a trailing string index.
OutputPatternStringSuffix(String, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternStringSuffix: Creates without a prefix.
OutputPatternStringSuffix(String, boolean, String) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternStringSuffix: Creates with a prefix.
outputSelectParam(CommandLine, String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Can point to either: a path ending in .xml, assumed to BeanXML for an output manager a directory, set as the outputDirectory in the input-context
outputsEnabled() - Method in class org.anchoranalysis.io.output.outputter.Outputter
OutputSequence - Interface in org.anchoranalysis.io.generator.sequence: A sequence of elements that are written to the same directory.
OutputSequenceFactory<T> - Class in org.anchoranalysis.io.generator.sequence: Creates and starts a OutputSequence with a particular generator and context.
OutputSequenceFactory(Generator<T>, OutputterChecked) - Constructor for class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
OutputSequenceIncrementing<T> - Class in org.anchoranalysis.io.generator.sequence: A sequence of outputs that use the same generator, where each output increments an index by one in the filename.
OutputSequenceIncrementing(BoundOutputter<T>, int) - Constructor for class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing
OutputSequenceIndexed<T,S> - Class in org.anchoranalysis.io.generator.sequence: A sequence of outputs that use the same generator with non-incrementing indexes for each output.
outputSharedObjects(MPPInitParams, OutputterChecked) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
OutputtedFile - Class in org.anchoranalysis.io.manifest.file: An entry in a Manifest for an outputted file from an experiment.
OutputtedFile(MutableDirectory, String, String, String, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.manifest.file.OutputtedFile
OutputtedFile(MutableDirectory, String, String, String, ManifestDescription) - Constructor for class org.anchoranalysis.io.manifest.file.OutputtedFile
Outputter - Class in org.anchoranalysis.io.output.outputter: Like OutputterChecked but exceptions are reported in a ErrorReporter.
Outputter(OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.io.output.outputter.Outputter
OutputterChecked - Class in org.anchoranalysis.io.output.outputter: A particular directory on the filesystem in which outputting can occur.
OutputterDirectories - Class in org.anchoranalysis.mpp.segment.define: Directories into which collections of different types of objects are written to in a define experiment
OutputterTarget - Class in org.anchoranalysis.io.output.outputter.directory: The directory and prefix an outputter writes to.
OutputterTarget(DirectoryWithPrefix, boolean) - Constructor for class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
outputToWriter(PrintWriter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
outputToWriter(PrintWriter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
OutputWriteFailedException - Exception in org.anchoranalysis.io.output.error
OutputWriteFailedException(String) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
OutputWriteFailedException(String, AnchorCombinableException) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
OutputWriteFailedException(String, HasFriendlyErrorMessage) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
OutputWriteFailedException(Throwable) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
OutputWriteSettings - Class in org.anchoranalysis.io.output.bean: Settings for how to write output, including default writers.
OutputWriteSettings() - Constructor for class org.anchoranalysis.io.output.bean.OutputWriteSettings
outsideAtThreshold - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
OutsideRange - Class in org.anchoranalysis.plugin.image.feature.bean.score
OutsideRange() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
OverlapCalculator - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce: Calculates overlap between object-masks
OverlapMaskBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapMaskBase() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
OverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapMIPBase() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
OverlapNumVoxels - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapNumVoxels() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxels
OverlapNumVoxelsMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapNumVoxelsMask() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxelsMask
overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
OverlappingObject<T> - Class in org.anchoranalysis.image.core.object.label: An object-mask that is founded to overlap with another during labelling.
OverlappingObject(T, ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.label.OverlappingObject
OverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
OverlapRatioMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapRatioMask() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
OverlapRelative - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Expresses the number of intersecting pixels between two objects as a ratio to something else (denominator)
OverlapRelative() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
OverlapRelativeToFirst - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
OverlapRelativeToFirst() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToFirst
OverlapRelativeToMaxVolume - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Overlap ratio to the maximum number of pixels
OverlapRelativeToMaxVolume() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMaxVolume
OverlapRelativeToMerged - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
OverlapRelativeToMerged() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMerged
OverlapRelativeToSecond - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
OverlapRelativeToSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToSecond
overlapScoreFor(ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
overlapScoreFor(BoundingBox, BoundingBox) - Method in class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes: The Intersection over Union (IoU) score for two bounding-boxes
overlapScoreFor(T, T) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression: A score calculating the overlap between two elements.
OverlapUtilities - Class in org.anchoranalysis.mpp.overlap
overlapWith(VoxelizedMarkMemo, VoxelizedMarkMemo, int) - Static method in class org.anchoranalysis.mpp.overlap.OverlapUtilities
overlapWithGlobalMask(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
overlapWithMaskGlobal(VoxelizedMarkMemo, VoxelizedMarkMemo, int, Voxels<UnsignedByteBuffer>, byte) - Static method in class org.anchoranalysis.mpp.overlap.OverlapUtilities: Counts the number of overlapping voxels between two VoxelizedMarkMemo
Overlay - Class in org.anchoranalysis.image.bean.spatial.arrange
Overlay - Class in org.anchoranalysis.overlay
Overlay() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Overlay
Overlay() - Constructor for class org.anchoranalysis.overlay.Overlay
overlayBufferedImage(BufferedImage, BufferedImage, int, int) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageOverlay
OverlayCollection - Class in org.anchoranalysis.overlay.collection
OverlayCollection() - Constructor for class org.anchoranalysis.overlay.collection.OverlayCollection
OverlayCollection(Stream<Overlay>) - Constructor for class org.anchoranalysis.overlay.collection.OverlayCollection
OverlayCollectionMarkFactory - Class in org.anchoranalysis.mpp.overlay: Two-way factory.
OverlayCollectionObjectFactory - Class in org.anchoranalysis.overlay.collection: Two-way factory.
OverlayMark - Class in org.anchoranalysis.mpp.overlay
OverlayMark(Mark, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.overlay.OverlayMark
OverlayObjectMask - Class in org.anchoranalysis.overlay.object
OverlayObjectMask(ObjectMask, int) - Constructor for class org.anchoranalysis.overlay.object.OverlayObjectMask
OverlayProperties - Class in org.anchoranalysis.overlay
OverlayProperties() - Constructor for class org.anchoranalysis.overlay.OverlayProperties

P

Padding - Class in org.anchoranalysis.image.bean.spatial: Padding (whitespace of certain extent) placed around an object in XY direction and in Z direction.
Padding() - Constructor for class org.anchoranalysis.image.bean.spatial.Padding
PairedWithMask - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared: Evaluates the object as a pair-feature together with the binary-mask from the shard objects.
PairedWithMask() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
PairNeighbors - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine: Creates a set of features, that creates pairs of neighboring-objects and applies a mixture of single-object features and pair features.
PairNeighbors() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
PairPxlMarkMemo - Class in org.anchoranalysis.mpp.pair
PairPxlMarkMemo(VoxelizedMarkMemo, VoxelizedMarkMemo) - Constructor for class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
PairsTableCalculator - Class in org.anchoranalysis.image.feature.session.merged: A feature-session to evaluate pairs of objects.
PairsTableCalculator(MergedPairsFeatures) - Constructor for class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
PairsTableCalculator(MergedPairsFeatures, MergedPairsInclude, boolean) - Constructor for class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
Pairwise - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
Pairwise() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
ParallelProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor: Executes jobs in parallel
ParallelProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
Param<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.operator.feature.bean: Extracts a key-value-param as a double
Param() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.Param
ParametersAsFeatures<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list: Loads a KeyValueParams as features.
ParametersAsFeatures() - Constructor for class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
ParametersExperiment - Class in org.anchoranalysis.experiment.task: Parameters for executing a task, when the manifest, log etc.
ParametersExperiment(ExperimentExecutionArguments, String, Optional<Manifest>, OutputterChecked, PathPrefixer, StatefulMessageLogger, boolean) - Constructor for class org.anchoranalysis.experiment.task.ParametersExperiment
ParametersUnbound<T,S> - Class in org.anchoranalysis.experiment.task
ParametersUnbound(ParametersExperiment, T, S, boolean) - Constructor for class org.anchoranalysis.experiment.task.ParametersUnbound
ParamFromCollection<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.shared: Retrieves a parameter from a collection in shared-objects.
ParamFromCollection() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
params() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
ParamsBean<T> - Class in org.anchoranalysis.bean.shared.params
ParamsBean() - Constructor for class org.anchoranalysis.bean.shared.params.ParamsBean
paramsDeriver() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
ParamsInitializer<T> - Interface in org.anchoranalysis.bean.initializable.params
parseAndRun(String[], LauncherConfig) - Method in class org.anchoranalysis.launcher.parser.ParseArgumentsAndRunExperiment: Parses the arguments to a command-line experiment and runs an experiment
ParseArgumentsAndRunExperiment - Class in org.anchoranalysis.launcher.parser: A general parser for command-line applications with certain attributes.
ParseArgumentsAndRunExperiment(Logger) - Constructor for class org.anchoranalysis.launcher.parser.ParseArgumentsAndRunExperiment
ParsedFilePathBag - Class in org.anchoranalysis.plugin.io.multifile
ParsedFilePathBag() - Constructor for class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
PartitionedMarks - Class in org.anchoranalysis.plugin.mpp.segment.optimization: Binary partition of marks into "available" and "accepted"
PartitionedMarks(MarkCollection, ToDoubleFunction) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks: Constructor
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.FilePath
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
path(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DirectoryMatch
pathCreator() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
PathCreator - Interface in org.anchoranalysis.io.output.path.prefixer: Converts file-paths between relative and absolute.
pathCurrentJAR(Class<?>) - Static method in class org.anchoranalysis.launcher.PathCurrentJarUtilities: Determines the path to the current jar directory (or folder with class files) so we can resolve a properties file
PathCurrentJarUtilities - Class in org.anchoranalysis.launcher
PathDifference - Class in org.anchoranalysis.core.system.path: Calculates the "difference" between a path and a base
PathDifferenceException - Exception in org.anchoranalysis.core.system.path
PathDifferenceException(String) - Constructor for exception org.anchoranalysis.core.system.path.PathDifferenceException
PathDifferenceException(String, Exception) - Constructor for exception org.anchoranalysis.core.system.path.PathDifferenceException
pathForBinding() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
pathForBinding() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
pathForBinding() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
pathForBinding() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
pathForBinding() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
pathForBinding() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
pathForBinding() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
pathForBinding() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
pathFromArgument(String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.ArgumentConverter: Converts the string passed as a command-line argument to a path.
PathFromGenerator - Class in org.anchoranalysis.plugin.annotation.bean.strategy
pathOrDirectory(String[], boolean) - Static method in class org.anchoranalysis.launcher.executor.selectparam.io.OutputFactory: If the argument is a path to a directory, then this directory is set as the default.
pathOrDirectoryOrGlobOrExtension(String[]) - Static method in class org.anchoranalysis.launcher.executor.selectparam.io.InputFactory
pathOrTaskName(String[], Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.task.TaskFactory: If the argument a name (no extension, no root, no special-chars apart from forward-slashes), then construct an automatic path to the tasks in the configuration directory.
pathOrTaskNameOrDefault(CommandLine, String, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Can point to either a path to beanXML
PathPrefixer - Class in org.anchoranalysis.io.output.bean.path.prefixer
PathPrefixer() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
PathPrefixerAvoidResolve - Class in org.anchoranalysis.io.output.bean.path.prefixer: A file-path-resolver that adds additional methods that perform the same function but output a relative-path rather than an absolute path after fully resolving paths
PathPrefixerAvoidResolve() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
PathPrefixerAvoidResolve(String) - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
PathPrefixerException - Exception in org.anchoranalysis.io.output.path.prefixer
PathPrefixerException(String) - Constructor for exception org.anchoranalysis.io.output.path.prefixer.PathPrefixerException
PathPrefixerException(Throwable) - Constructor for exception org.anchoranalysis.io.output.path.prefixer.PathPrefixerException
PathRegEx - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer: Matches a regex against incoming file-paths to form a prefix for output
PathRegEx() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx
pathRelativeProperties() - Method in class org.anchoranalysis.launcher.config.LauncherConfig: path to a property file that defines a relative-path to the default experiment in bean XML
pathRelativeToBean(AnchorBean<?>, String) - Static method in class org.anchoranalysis.bean.xml.factory.BeanPathUtilities
PatternSpan - Class in org.anchoranalysis.plugin.io.bean.descriptivename.patternspan: Finds a pattern in the descriptive name, and uses the region from the first variable to the last-variable as the descriptive-name
PatternSpan() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.patternspan.PatternSpan
PayloadCalculator - Interface in org.anchoranalysis.image.feature.evaluator
percentAnnotatedImages() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
percentGreaterEqualTo(int) - Method in class org.anchoranalysis.math.histogram.Histogram
percentLeftMatched() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
percentRightMatched() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
percentSkippedAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.AddConstant
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase: The binary arithmetic operation that combines the voxel-value and the constant-value
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyConstant
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractFromConstant
periodEnd(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiver
periodEnd(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
PeriodicSubdirectoryReporter<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
PeriodicSubdirectoryReporter() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
PeriodReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.period
PeriodReceiverException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.period
PeriodReceiverException() - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverException
PeriodReceiverException(Exception) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverException
PeriodReceiverException(String) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverException
PeriodReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.period
PeriodReceiverList() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
periodStart(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiver
periodStart(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
PeriodTriggerBank<S> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.period
PeriodTriggerBank() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
permissive() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: A writer that allows all output-names, and records the written output-names
Permissive - Class in org.anchoranalysis.io.output.bean.rules: Allows all output-names to be outputted in both first and second level.
Permissive() - Constructor for class org.anchoranalysis.io.output.bean.rules.Permissive
PermissiveExcept - Class in org.anchoranalysis.io.output.bean.rules: All outputs are enabled except particular ones.
PermissiveExcept() - Constructor for class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
PermissiveExcept(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.PermissiveExcept: Create with first-level output names
PermutationSetter - Interface in org.anchoranalysis.bean.permute.setter: Imposes a permutation on some property of a bean.
PermutationSetterException - Exception in org.anchoranalysis.bean.permute.setter
PermutationSetterException(String) - Constructor for exception org.anchoranalysis.bean.permute.setter.PermutationSetterException
PermutationSetterList - Class in org.anchoranalysis.bean.permute.setter: Applies several permutation setters to the same object
PermutationSetterList() - Constructor for class org.anchoranalysis.bean.permute.setter.PermutationSetterList
PermutationSetterSingle - Class in org.anchoranalysis.bean.permute.setter: Sets a permutation from a list of fields
PermutationSetterSingle() - Constructor for class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
PermutationSetterSingle(Field) - Constructor for class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
PermutationSetterUtilities - Class in org.anchoranalysis.bean.permute.setter
Permute - Class in org.anchoranalysis.plugin.image.bean.object.provider: Permutes some changes over an ObjectCollectionProvider and collects all the results in an ObjectCollection
Permute() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Permute
PermuteDivideByParam<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
PermuteDivideByParam() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
PermuteFeature<S,T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes one or more properties of a Feature, so as to create a set of Features
PermuteFeature() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
PermuteFeatureBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Creates permutations of a feature by modifying a particular property of it in different ways.
PermuteFeatureBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
PermuteFeatureSequenceInteger<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Permutes a property on a feature with a sequence of integers.
PermuteFeatureSequenceInteger() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
PermuteFirstSecondOrder<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
PermuteFirstSecondOrder(PermuteFirstSecondOrder.CreateFirstSecondOrder<T>, double, double) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
PermuteFirstSecondOrder.CreateFirstSecondOrder<T extends FeatureInput> - Interface in org.anchoranalysis.plugin.image.feature.bean.list.permute
PermuteGaussianScore<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
PermuteGaussianScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteGaussianScore
PermuteProperty<T> - Class in org.anchoranalysis.bean.permute.property
PermuteProperty() - Constructor for class org.anchoranalysis.bean.permute.property.PermuteProperty
PermutePropertyDescribeIndex - Class in org.anchoranalysis.bean.permute.property: Proxies an existing PermuteProperty but replaces the existing naming behaviour
PermutePropertyDescribeIndex() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
PermutePropertyDoubleSet - Class in org.anchoranalysis.bean.permute.property
PermutePropertyDoubleSet() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
PermutePropertySequence<T> - Class in org.anchoranalysis.bean.permute.property: Base class for permute-properties involving a sequence of numbers
PermutePropertySequence() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequence
PermutePropertySequenceDouble - Class in org.anchoranalysis.bean.permute.property: An arithmetic sequence of doubles, obtained by dividing an integer sequence by a divider
PermutePropertySequenceDouble() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
PermutePropertySequenceDouble.DoubleRange - Class in org.anchoranalysis.bean.permute.property
PermutePropertySequenceInteger - Class in org.anchoranalysis.bean.permute.property: An arithmetic sequence of doubles, obtained by dividing an integer sequence by a divider
PermutePropertySequenceInteger() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
PermutePropertySequenceIntegerWithinString - Class in org.anchoranalysis.bean.permute.property
PermutePropertySequenceIntegerWithinString() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
PermutePropertyStringSet - Class in org.anchoranalysis.bean.permute.property
PermutePropertyStringSet() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
PermutePropertyWithPath<T> - Class in org.anchoranalysis.bean.permute.property: Base classes for PermuteProperty that require a path
PermutePropertyWithPath() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
PermuteZScore<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute: Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
PermuteZScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteZScore
Plot<T> - Class in org.anchoranalysis.plot.bean: Defines a plot as a function of data and axis-limits.
Plot() - Constructor for class org.anchoranalysis.plot.bean.Plot
PlotAxisLabels - Class in org.anchoranalysis.plot.index: Labels for x and y axis in graph
PlotAxisLabels() - Constructor for class org.anchoranalysis.plot.index.PlotAxisLabels
PlotColorScheme - Class in org.anchoranalysis.plot.bean.colorscheme
PlotColorScheme() - Constructor for class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
PlotHistogram - Class in org.anchoranalysis.plugin.image.bean.stack.provider.plot: Plots a histogram onto a stack.
PlotHistogram() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
PlotIndexBase<T,S extends org.jfree.data.general.Dataset> - Class in org.anchoranalysis.plot.index
PlotIndexBase(String, String[]) - Constructor for class org.anchoranalysis.plot.index.PlotIndexBase: Constructor
PlotIndexBaseCategorical<T,S extends org.jfree.data.category.CategoryDataset> - Class in org.anchoranalysis.plot.index: Base class for plots involving categorical data types.
PlotIndexBaseCategorical(String, String[], GetForSeries<T, String>, GetForSeries<T, Paint>) - Constructor for class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
PlotInstance - Class in org.anchoranalysis.plot: A Plot combined with data and parameters, ready to be displayed.
PlotInstance(JFreeChart, Optional<AxisLimits>) - Constructor for class org.anchoranalysis.plot.PlotInstance
pluralize(String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities: Given something, returns somethings
pluralizeMaybe(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities: Returns something or somethings depending on the number
PNG - Class in org.anchoranalysis.io.imagej.bean.stack.writer: Writes a PNG image using ImageJ.
PNG() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
point(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Is this point within the bounding-box?
Point2d - Class in org.anchoranalysis.spatial.point
Point2d() - Constructor for class org.anchoranalysis.spatial.point.Point2d
Point2d(double, double) - Constructor for class org.anchoranalysis.spatial.point.Point2d
Point2d(Point2d) - Constructor for class org.anchoranalysis.spatial.point.Point2d
Point2f - Class in org.anchoranalysis.spatial.point
Point2f() - Constructor for class org.anchoranalysis.spatial.point.Point2f
Point2f(float, float) - Constructor for class org.anchoranalysis.spatial.point.Point2f
Point2i - Class in org.anchoranalysis.spatial.point
Point2i() - Constructor for class org.anchoranalysis.spatial.point.Point2i
Point2i(int, int) - Constructor for class org.anchoranalysis.spatial.point.Point2i
Point2i(Point2i) - Constructor for class org.anchoranalysis.spatial.point.Point2i: Copy constructor.
Point3d - Class in org.anchoranalysis.spatial.point
Point3d() - Constructor for class org.anchoranalysis.spatial.point.Point3d
Point3d(double, double, double) - Constructor for class org.anchoranalysis.spatial.point.Point3d
Point3d(Point3f) - Constructor for class org.anchoranalysis.spatial.point.Point3d
Point3d(Tuple3d) - Constructor for class org.anchoranalysis.spatial.point.Point3d
Point3d(Vector3d) - Constructor for class org.anchoranalysis.spatial.point.Point3d
Point3f - Class in org.anchoranalysis.spatial.point
Point3f() - Constructor for class org.anchoranalysis.spatial.point.Point3f
Point3f(float, float, float) - Constructor for class org.anchoranalysis.spatial.point.Point3f
Point3f(Point3f) - Constructor for class org.anchoranalysis.spatial.point.Point3f
Point3i - Class in org.anchoranalysis.spatial.point
Point3i() - Constructor for class org.anchoranalysis.spatial.point.Point3i: Creates the points with a 0 in each dimension
Point3i(int, int, int) - Constructor for class org.anchoranalysis.spatial.point.Point3i
Point3i(ReadableTuple3i) - Constructor for class org.anchoranalysis.spatial.point.Point3i
PointClipper - Class in org.anchoranalysis.mpp.points: Ensures a point has values contained inside image-dimensions
PointConverter - Class in org.anchoranalysis.spatial.point: Conversion utilities between different types and dimensionalities of points
pointIgnoreZ(Point3i) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Is this point within the bounding-box, but ignoring the z-dimension?
PointList - Class in org.anchoranalysis.mpp.mark.points
PointList() - Constructor for class org.anchoranalysis.mpp.mark.points.PointList
PointList(Stream<Point3d>) - Constructor for class org.anchoranalysis.mpp.mark.points.PointList
pointListAtFirstPoint(List<Point3i>) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels: Sets all points in a list, to point at the first point (the root point) in the list
PointListBase - Class in org.anchoranalysis.mpp.mark.points
PointListBase() - Constructor for class org.anchoranalysis.mpp.mark.points.PointListBase
PointListBase(Stream<Point3d>) - Constructor for class org.anchoranalysis.mpp.mark.points.PointListBase
PointListFactory - Class in org.anchoranalysis.mpp.mark.points
pointOnOutline(Point3d, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutline
pointOnOutline(Point3d, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
PointRange - Class in org.anchoranalysis.spatial.box: Keeps track of the range experienced by points in the x, y and z dimensions
PointRange() - Constructor for class org.anchoranalysis.spatial.box.PointRange
points() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath: The points associated with the path
points() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
PointSampler - Interface in org.anchoranalysis.mpp.probmap
PointsBean<T> - Class in org.anchoranalysis.mpp.bean.points
PointsBean() - Constructor for class org.anchoranalysis.mpp.bean.points.PointsBean
pointsDiscrete() - Method in class org.anchoranalysis.spatial.Contour
PointsFitter - Class in org.anchoranalysis.mpp.bean.points.fitter
PointsFitter - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks
PointsFitter() - Constructor for class org.anchoranalysis.mpp.bean.points.fitter.PointsFitter
PointsFitter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
PointsFitterException - Exception in org.anchoranalysis.mpp.bean.points.fitter
PointsFitterException(Exception) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.PointsFitterException
PointsFitterException(String) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.PointsFitterException
PointsFitterFromObjects - Class in org.anchoranalysis.plugin.points.bean.mark.provider.collection
PointsFitterFromObjects() - Constructor for class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
PointsFitterToMark - Class in org.anchoranalysis.plugin.points.bean.fitter
PointsFitterToMark() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
pointsFromContour(ObjectMask) - Static method in class org.anchoranalysis.plugin.points.bean.contour.PointsFromContourTraverser: Extracts a list of points from the outline (contour) of the object-mask
PointsFromContourTraverser - Class in org.anchoranalysis.plugin.points.bean.contour
PointsFromMask - Class in org.anchoranalysis.image.core.points
PointsFromObject - Class in org.anchoranalysis.image.core.points
PointsFromObjects - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
PointsFromObjects() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
PointsFromOrientationProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
PointsFromOrientationProposer() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
PointsInitParams - Class in org.anchoranalysis.mpp.bean.init
PointsNeighborChecker - Class in org.anchoranalysis.image.core.points
pointsOnAllOutlines(ObjectCollection) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities
pointsOnOutline(ObjectMask) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities
PointsProposer - Class in org.anchoranalysis.mpp.bean.proposer
PointsProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.PointsProposer
PointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer: Like a IntConsumer but accepts two coordinates of a point as scalar arguments.
Polygon - Class in org.anchoranalysis.mpp.mark.points
Polygon() - Constructor for class org.anchoranalysis.mpp.mark.points.Polygon
PolygonCurve - Class in org.anchoranalysis.mpp.mark.points
PolygonCurve() - Constructor for class org.anchoranalysis.mpp.mark.points.PolygonCurve
populate(List<NamedBean<FeatureListProvider<FeatureInput>>>, Logger) - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
populate(PropertyInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
populate(PropertyInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
populate(PropertyInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle2D
populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle3D
populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAxisAngle
populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory: Populates a newly created matrix.
populateFrom(Stack, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
populateMissingFromArbitrarySlice(Stack) - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
PopulateStoreFromDefine<V extends BeanInitParams> - Class in org.anchoranalysis.image.bean.nonbean.init: Helps populates a NamedProviderStore from the contents of a Define.
PopulateStoreFromDefine(Define, PropertyInitializer<?>, Logger) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine: Constructor
position() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: The position of the buffer ala Buffer.position.
position(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Assigns a new position to the buffer.
position(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Assigns a new position to the buffer.
Position - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
Position() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
PositionProposer - Class in org.anchoranalysis.mpp.bean.proposer
PositionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.PositionProposer
Positive - Annotation Type in org.anchoranalysis.bean.annotation: The bean-field should have a value > 0.
possibleOverlappingObjects(ObjectMask, Iterable<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
possibleOverlappingObjects(ObjectMask, Iterable<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
possibleOverlappingObjects(BoundingBox, Iterable<WithConfidence<BoundingBox>>) - Method in class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes: As bounding box intersection test is cheap, we pass back all neighbors
possibleOverlappingObjects(T, Iterable<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy: Finds a subset of others that possibly overlap with the source element.
precalculate(ObjectWithProperties, Dimensions) - Method in class org.anchoranalysis.overlay.bean.DrawObject
precalculate(ColoredOverlayCollection, DrawOverlay, Dimensions, BinaryValuesByte) - Static method in class org.anchoranalysis.overlay.writer.DrawOverlay
PrecalculationOverlay - Class in org.anchoranalysis.overlay.writer: Overlays with additional pre-calculations that make them quicker to draw onto a RGBStack
PrecalculationOverlay(ObjectWithProperties) - Constructor for class org.anchoranalysis.overlay.writer.PrecalculationOverlay
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate: A precondition, which if evaluates to false, cancels the filter i.e.
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfNotEmpty
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase: If this evaluates true, the mask will be returned as-is, otherwise maskElse is returned
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
PredicateAtCorner - Class in org.anchoranalysis.image.voxel.extracter.predicate: Projects a VoxelsPredicate to a corner in a larger global space
PredicateAtCorner(ReadableTuple3i, VoxelsPredicate) - Constructor for class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
PredicateBufferBinary<T> - Interface in org.anchoranalysis.image.voxel.iterator.predicate.buffer: Like ProcessBufferBinary but returns a boolean.
PredicateImplementation<T> - Class in org.anchoranalysis.image.voxel.extracter.predicate: Implementation of VoxelsPredicate for a particular Voxels.
PredicateImplementation(Voxels<T>, Predicate<T>) - Constructor for class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
PredicateTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.predicate: Like Predicate but takes two bytes as argument.
prefer(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Prefer to keep descriptor whose input-class is a sub-class rather than a super-class
prefer(Feature<?>, Feature<?>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Like FeatureInputType.prefer(Class, Class) but accepts features directly as input.
prefixPluralize(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities: Returns n somethings
prefixPluralizeMaybe(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities: Returns 1 something or n somethings as is appropriate
Prepend - Class in org.anchoranalysis.bean.shared.color.scheme
Prepend() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Prepend
PrependName - Class in org.anchoranalysis.feature.bean.list: Prepends a string to each feature in the list
PrependName() - Constructor for class org.anchoranalysis.feature.bean.list.PrependName
PreserveName - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
PreserveName() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
prettyPath(String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.PrettyPathConverter: Converts to either a normalized absolute-path or relative-path depending on which is prettier to the user
prettyPath(Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.PrettyPathConverter: Converts to either a normalized absolute-path or relative-path depending on which is prettier to the user
PrettyPathConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path
previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
previousEqualIndex(int) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncomplete
previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
previousIndex(int) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncomplete
previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
primaryReport() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.StateReporter
primaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterIdentity
primaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
primaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
PrimitiveConverter - Class in org.anchoranalysis.image.voxel.buffer.primitive: Type conversion between primitive data types.
PrincipalAxisEccentricity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: Calculates the eccentricity of the Principal Axes (as defined by Image Moments)
PrincipalAxisEccentricity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
PrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: The length of a principal-axis (as defined by Image Moments).
PrincipalAxisLength() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
PrincipalAxisOrientation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: An element from orientation of a principal-axis (as defined by Image Moments).
PrincipalAxisOrientation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
printAllFilesFromTestFolderPath(String) - Method in class org.anchoranalysis.test.TestLoader: Prints the names of all files (recursively) in a test-folder to stdout
PrioritisedVertex - Class in org.anchoranalysis.plugin.image.object.merge.priority: A vertex with a priority attached, and a boolean flag as to whether it can be merged or not
PrioritisedVertex(ObjectMask, double, double, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex: Constructor
Prioritizer - Interface in org.anchoranalysis.plugin.image.object.merge.priority: Creates a priority between two vertices
PriorityQueueIndexRangeDownhill<T> - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding: Implements a priority queue based upon a range of values from 0 to maxValue,
PriorityQueueIndexRangeDownhill(int) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
ProbabilityMap - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position: Uses a probability field defined over the voxels to make some positions more likely than others
ProbabilityMap() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
probCalculator(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
probCalculator(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
probCalculator(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
ProbMap - Interface in org.anchoranalysis.mpp.probmap
ProbMapObjects - Class in org.anchoranalysis.mpp.probmap: TODO this doesn't seem currently used.
ProbMapObjects(ObjectCollection, Dimensions) - Constructor for class org.anchoranalysis.mpp.probmap.ProbMapObjects
ProbWeights - Class in org.anchoranalysis.mpp.probmap
ProbWeights() - Constructor for class org.anchoranalysis.mpp.probmap.ProbWeights
process(byte, byte) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessTwoBytes
process(Channel, Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
process(Channel, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.TwoVoxelMappingBase
process(Channel, Channel, Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
process(Channel, Channel, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MeanThreeChannels
process(VoxelBuffer<S>, VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinaryWithoutOffset: Processes a voxel location in a buffer
process(VoxelBuffer<S>, VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinary: Processes a voxel location in a buffer
process(VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferUnary: Processes a voxel location in a buffer.
process(Point3i) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint
process(Point3i, VoxelBuffer<S>, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryMixed: Processes a voxel location in two buffers.
process(Point3i, VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferUnaryWithPoint: Processes a voxel location in a buffer.
process(Point3i, S, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinary: Processes a voxel location in two buffers.
process(Point3i, T, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferUnary: Processes a voxel location in a buffer
process(Point3i, T, T, T, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferTernary: Processes a voxel location in a buffer
process(S, T) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryWithoutOffset: Processes a voxel location in a buffer
process(T) - Method in interface org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP.OperationWithInitParams
process(T, EnergyStack) - Method in interface org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy.OperationWithEnergyStack
processAllPointsInNeighborhood(boolean, ProcessVoxelNeighbor<?>) - Method in interface org.anchoranalysis.image.voxel.neighborhood.Neighborhood
ProcessBufferBinary<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves two Buffer for the current z-slice.
ProcessBufferBinaryMixed<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves both one VoxelBuffer for the current z-slice and one Buffer for the current z-slice.
ProcessBufferBinaryWithoutOffset<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes two buffers for each z-slice jointly, without any offset or point.
ProcessBufferTernary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves three buffers for the current z-slice.
ProcessBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves a buffer for the current z-slice.
ProcessChangedPointAbsoluteMasked<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor: Processes a point which has been translated (changed) relative to another point - and includes global coordinates and includes an object-mask buffer
processEachSlice(Channel, Consumer<ImageProcessor>) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper: Applies a Consumer to each slice independently of a Channel.
processEachSlice(BinaryVoxels<UnsignedByteBuffer>, Consumer<ImageProcessor>) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper: Applies a Consumer to each slice independently of a BinaryVoxels<UnsignedByteBuffer>.
processInput(NamedChannelsForSeries, InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
processInput(InputOutputContext, Optional<NamedProvider<Stack>>, Optional<NamedProvider<ObjectCollection>>, Optional<KeyValueParams>, DefineOutputterMPPWithEnergy.OperationWithEnergyStack<MPPInitParams, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy
processInput(InputForMPPBean, InputOutputContext, DefineOutputterMPPWithEnergy.OperationWithEnergyStack<ImageInitParams, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy
processInput(MultiInput, InputProcessContext<FeatureTableCalculator<T>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
processInput(T, InputProcessContext<FeatureList<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
processInput(T, InputProcessContext<S>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Processes one input to generate features.
processInputImage(MultiInput, InputOutputContext, DefineOutputterMPP.OperationWithInitParams<ImageInitParams>) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
processInputMPP(MultiInput, InputOutputContext, DefineOutputterMPP.OperationWithInitParams<MPPInitParams>) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
ProcessOutputOptions - Class in org.anchoranalysis.launcher.options.outputs: Processes command-line options relating to additional outputs.
ProcessOutputOptions(CommandLineExtracter, ExperimentExecutionArguments) - Constructor for class org.anchoranalysis.launcher.options.outputs.ProcessOutputOptions
processOverlapping(WithConfidence<ObjectMask>, WithConfidence<ObjectMask>, Runnable, Consumer<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
processOverlapping(WithConfidence<T>, WithConfidence<T>, Runnable, Consumer<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
processOverlapping(WithConfidence<T>, WithConfidence<T>, Runnable, Consumer<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy: Processes an object that is deemed to overlap
processPixel(UnsignedByteBuffer, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityByteBuffer
processPixel(UnsignedShortBuffer, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityShortBuffer
processPixel(T, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
processPoint(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Processes a particular point
processPoint(int, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: Processes a particular point
processPoint(int, int, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: Processes a particular point
processPoint(int, int, int, int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
ProcessPoint - Interface in org.anchoranalysis.image.voxel.iterator.process: Processes a 3D point.
processStacks(NamedStacks, Optional<String>, GroupedSharedState<Channel, RunningSumChannel>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
processStacks(NamedStacks, Optional<String>, GroupedSharedState<Histogram, Histogram>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
processStacks(NamedStacks, Optional<String>, GroupedSharedState<S, T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Processes one set of named-stacks.
ProcessTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.process: Processes two bytes.
ProcessVoxelBufferBinary<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes a 3D point like ProcessPoint but also retrieves two VoxelBuffers for the current z-slice.
ProcessVoxelBufferBinaryWithoutOffset<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes two voxel-buffers for each z-slice jointly, without any offset or point.
ProcessVoxelBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes a 3D point like ProcessPoint but also retrieves a VoxelBuffer for the current z-slice.
ProcessVoxelBufferUnaryWithPoint<T,E extends Exception> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes a 3D point like ProcessVoxelBufferUnary but also exposes a Point3i.
ProcessVoxelNeighbor<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor: Processes a point that is an neighbor of another.
ProcessVoxelNeighborAbsolute<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor: Processes a point that is a neighbor of another - includes global (absolute) coordinates for this point.
ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.iterator.neighbor
ProcessVoxelNeighborAbsoluteWithSlidingBuffer(SlidingBuffer<?>) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
ProcessVoxelNeighborFactory - Class in org.anchoranalysis.image.voxel.iterator.neighbor
progressing() - Method in interface org.anchoranalysis.core.functional.checked.CheckedSupplier: An interface to a similar supplier that uses a progress-reporter
ProgressReporter - Interface in org.anchoranalysis.core.progress
ProgressReporterConsole - Class in org.anchoranalysis.core.progress
ProgressReporterConsole(int) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterConsole
ProgressReporterIncrement - Class in org.anchoranalysis.core.progress
ProgressReporterIncrement(ProgressReporter) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterIncrement
ProgressReporterMultiple - Class in org.anchoranalysis.core.progress
ProgressReporterMultiple(ProgressReporter, int) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterMultiple
ProgressReporterNull - Class in org.anchoranalysis.core.progress: Placeholder that doesn't measure any progress
ProgressReporterOneOfMany - Class in org.anchoranalysis.core.progress
ProgressReporterOneOfMany(ProgressReporterMultiple) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
ProgressReporterOneOfMany(ProgressReporterMultiple, int, int) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
projectMax() - Method in class org.anchoranalysis.image.core.channel.Channel
projectMax() - Method in class org.anchoranalysis.image.core.stack.DisplayStack: Maximum-intensity projection.
projectMax() - Method in class org.anchoranalysis.image.core.stack.Stack: Maximum intensity projection.
projectMax() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized: Maximum intensity projection.
projectMax() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A maximum-intensity projection (flattens in z dimension)
projectMax() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: A maximum intensity projection of all slices
projectMean() - Method in class org.anchoranalysis.image.core.channel.Channel
projectMean() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: A mean intensity projection of all slices
projectSlice(T) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer
projectSlice(T) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
PropertyDefiner - Interface in org.anchoranalysis.bean.initializable.property
PropertyInitializer - Class in org.anchoranalysis.bean.initializable.property: Tries to initialize a bean's property with particular (or derived) parameters
PropertyInitializer(Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.PropertyInitializer: Simpler case where only the current-parameters can be initialized, but for no further property-types.
PropertyInitializer(Class<?>, List<ExtractFromParam<P, ?>>) - Constructor for class org.anchoranalysis.bean.initializable.property.PropertyInitializer: More complex-case where both current-parameters and other extracted property-types can be initialized.
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty: An iterator (of size numPermutations()) with the values for the property
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
propertyValuesDefinitelyInteger() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
ProposalAbnormalFailureException - Exception in org.anchoranalysis.mpp.proposer: An exception when a proposal could not be made for an abnormal reason
ProposalAbnormalFailureException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException
ProposalAbnormalFailureException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException
ProposalAbnormalFailureException(Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException
proposalVisualization(boolean) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkProposer
proposalVisualization(boolean) - Method in class org.anchoranalysis.mpp.bean.proposer.PointsProposer
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
proposalVisualization(boolean, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ChooseOneList
proposalVisualization(boolean, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
proposalVisualization(boolean, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrderedList
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.proposer.ScalarProposer
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkCollectionProposer
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.CreateNew
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.proposer.OrientationProposer
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomXY
propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkProposer
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ChooseOneList
propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrderedList
propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkSplitProposer
propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
propose(ProposerContext) - Method in interface org.anchoranalysis.mpp.proposer.OptionalPointProposer
propose(ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
propose(ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
propose(ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class org.anchoranalysis.mpp.bean.proposer.radii.RadiiProposer
propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class org.anchoranalysis.mpp.bean.proposer.PointsProposer
propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
proposeKernel(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
proposeNewMarks(VoxelizedMarksWithEnergy, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
proposeNewMarks(MarksFromPartition, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
proposeNewMarks(T, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
proposer() - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
ProposerBean<T> - Class in org.anchoranalysis.mpp.bean.proposer
ProposerBean() - Constructor for class org.anchoranalysis.mpp.bean.proposer.ProposerBean
ProposerContext - Class in org.anchoranalysis.mpp.proposer
ProposerContext(RandomNumberGenerator, EnergyStack, RegionMap, ErrorNode) - Constructor for class org.anchoranalysis.mpp.proposer.ProposerContext
ProposerException - Exception in org.anchoranalysis.mpp.proposer: An exception thrown when something goes wrong in a Proposer
ProposerException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposerException
ProposerException(Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposerException
ProposerFailureDescription - Class in org.anchoranalysis.mpp.proposer.error
ProposerFailureDescription() - Constructor for class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
Provider<T> - Interface in org.anchoranalysis.bean.provider: A class (usually an AnchorBean} that creates or provides another obhect
ProviderAsStack - Interface in org.anchoranalysis.image.core.stack: Provides a stack
ProviderHolder<T> - Class in org.anchoranalysis.bean.provider: A convenient way of providing an object without using a AnchorBean.
ProviderHolder(T) - Constructor for class org.anchoranalysis.bean.provider.ProviderHolder
put(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
put(Class<? extends T>, T) - Method in class org.anchoranalysis.bean.BeanInstanceMap
put(String, double) - Method in class org.anchoranalysis.core.value.KeyValueParams
put(String, String) - Method in class org.anchoranalysis.core.value.KeyValueParams
put(String, CSVRow) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.MapGroupToRow
put(ByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Relative put-method from an unsigned byte buffer, represented by a ByteBuffer.
put(ShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Relative put-method from an unsigned short buffer, represented by a ShortBuffer.
put(K, V) - Method in class org.anchoranalysis.core.cache.LRUCache: Puts a key-value pair irrespective of whether its already present or not
put(UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Relative put-method from an unsigned byte buffer, represented by a UnsignedByteBuffer.
put(UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Relative put-method from an unsigned short buffer, represented by a UnsignedShortBuffer.
put(T, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
put(U, S) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
putAll(KeyValueParams) - Method in class org.anchoranalysis.core.value.KeyValueParams
putByte(int, byte) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Puts a byte in the buffer at a particular position, converting, if necessary, to the buffer type.
putCode(int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a double at the current buffer position.
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a double at a particular buffer position.
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putDoubleClipped(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts a double at the current buffer position, clipping to ensure the value is within the range (0,255).
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a float at the current buffer position.
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a float at a particular buffer position.
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putFloatClipped(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts a float at the current buffer position, clipping to ensure the value is within the range (0,255).
putFloatClipped(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts a float at the current buffer position, clipping to ensure the value is within the range (0,255).
putIfEmpty(String, double) - Method in class org.anchoranalysis.core.value.KeyValueParams
putInt(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Puts an int in the buffer at a particular position, converting, if necessary, to the buffer type.
putInt(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a long at the current buffer position.
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putLongClipped(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts a long at the current buffer position, clipping to ensure the value is within the range (0,255).
putRaw(byte) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts an unsigned-byte (represented as a byte) at the current buffer position.
putRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented as a int) at the current buffer position.
putRaw(int, byte) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts an unsigned-byte (represented as a byte) a particular buffer position.
putRaw(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented as a int) a particular buffer position.
putRaw(int, short) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts an unsigned-short (represented as a short) a particular buffer position.
putRaw(short) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts an unsigned-short (represented as a short) at the current buffer position.
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Puts an unsigned-byte (represented by an int) at current buffer position.
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Puts an unsigned-byte (represented as a int) a particular buffer position.
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putUnsigned(int, long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented as a long) a particular buffer position.
putUnsigned(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented by a long) at current buffer position.
putUnsignedClipped(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts a long at the current buffer position, clipping to ensure the value is within the range (0,255).
putUnsignedInt(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts an unsigned-int (represented by a int) at current buffer position.
PxlListOperationFromMark - Class in org.anchoranalysis.mpp.feature.bean.mark
PxlListOperationFromMark() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.PxlListOperationFromMark
PxlMarkMemoFactory - Class in org.anchoranalysis.mpp.mark.voxelized.memo

Q

QuadraticEquationSolver - Class in org.anchoranalysis.math.equation: Solves a Quadratic Equation by finding non-complex roots
QuadraticEquationSolver.QuadraticRoots - Class in org.anchoranalysis.math.equation: Roots (solution) of a quadratic equation
QuadraticRoots(double, double) - Constructor for class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
quantile(double) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
quantile(double) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
quantile(double) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
quantile(double) - Method in class org.anchoranalysis.math.histogram.Histogram
Quantile - Class in org.anchoranalysis.feature.bean.results: The quantile of the results from a particular feature.
Quantile - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Calculates the threshold value from a quantile of a histogram.
Quantile - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Quantile() - Constructor for class org.anchoranalysis.feature.bean.results.Quantile
Quantile() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
Quantile() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
quantileAboveZero(double) - Method in class org.anchoranalysis.math.histogram.Histogram
QuantileAcrossConnectedComponents - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object: Calculates the median of a feature applied to each connected component
QuantileAcrossConnectedComponents() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
QuantileAcrossObjects<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates the quantile of a feature applied to each connected component
QuantileAcrossObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
QuantileIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel
QuantileIntensity(double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.QuantileIntensity
QuantileIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram: Scales by a quantile of the intensity values of an image.
QuantileIntensityFromHistogram(double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
QuantileStretch - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data range
QuantileStretch() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
QuickBase<T extends InputFromManager> - Class in org.anchoranalysis.plugin.quick.bean.input: A base for quick managers that make various assumptions about file-structure.
QuickBase() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.QuickBase
QuickExperiment<S> - Class in org.anchoranalysis.plugin.quick.bean.experiment: A quick way of defining an InputOutputExperiment where several assumptions are made.
QuickExperiment() - Constructor for class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
QuickMultiDatasetExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.quick.bean.experiment: Makes a lot of assumptions, that allows us to reduce the number of inputs to an InputOutputExperiment.
QuickMultiDatasetExperiment() - Constructor for class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
QuickMultiDatasetStructuredExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.quick.bean.structure: Similar to QuickMultiDatasetStructuredExperiment put sets properties according to an expected directory structure.
QuickMultiDatasetStructuredExperiment() - Constructor for class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.Mark: An alternative "quick" metric for overlap for a mark
QuickOverlapCalculation - Interface in org.anchoranalysis.mpp.mark: A method to quickly calculate overlap approximately

R

RadiiMinRatio - Class in org.anchoranalysis.plugin.mpp.bean.check
RadiiMinRatio() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
radiiOrdered() - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
radiiOrderedResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
RadiiProposer - Class in org.anchoranalysis.mpp.bean.proposer.radii
RadiiProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.radii.RadiiProposer
RadiiProposerRepeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.radii
RadiiProposerRepeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
RadiiRandomizer - Class in org.anchoranalysis.mpp.mark.conic: Utility functions for generating random radii for ConicBase
RadiiRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
RadiiRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
radiusForRegion(int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
radiusForRegionSquared(int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
RandomCollection<T> - Class in org.anchoranalysis.mpp.pair: A collection of items from which one can randomly sample
RandomCollection() - Constructor for class org.anchoranalysis.mpp.pair.RandomCollection
RandomCollectionWithAddCriteria<T> - Class in org.anchoranalysis.mpp.feature.addcriteria: An implementation of a RandomCollection that uses AddCriteria
RandomCollectionWithAddCriteria(Class<?>) - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
randomIndex(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
randomizeRadii(Bound, RandomNumberGenerator, Optional<Resolution>, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.RadiiRandomizer
randomMark(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
RandomNumberGenerator - Interface in org.anchoranalysis.core.random: Generates random numbers from various distributions.
RandomNumberGeneratorBean - Class in org.anchoranalysis.bean.shared.random
RandomNumberGeneratorBean() - Constructor for class org.anchoranalysis.bean.shared.random.RandomNumberGeneratorBean
RandomNumberGeneratorMersenne - Class in org.anchoranalysis.core.random: Implements a random-number generator using the MersenneTwister algorithm.
RandomNumberGeneratorMersenne(boolean) - Constructor for class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
RandomOrder - Class in org.anchoranalysis.plugin.io.bean.provider.file
RandomOrder() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.RandomOrder
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.bound.OrientableBounds
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
RandomOrientation - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
RandomOrientation() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
RandomOrientation(RotationBounds) - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
RandomXY - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
RandomXY() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomXY
randOpen(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound: A random value between the bounds (open interval)
range() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence
Range - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic: The range (difference in values) between two quantiles
Range<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range.feature: The statistical range between two values i.e.
Range() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
Range() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
rangeChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
RangeCompareBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
RangeCompareBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
RangeCompareFromScalars<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range: A base-class for setting the boundaries of the range using constant scalars
RangeCompareFromScalars() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
rangeCPresent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
rangeLimitsIfEmpty(DefaultCategoryDataset) - Method in class org.anchoranalysis.plot.index.BarPlot
rangeLimitsIfEmpty(DefaultBoxAndWhiskerCategoryDataset) - Method in class org.anchoranalysis.plot.index.BoxPlot
rangeLimitsIfEmpty(XYDataset) - Method in class org.anchoranalysis.plot.index.LinePlot
rangeLimitsIfEmpty(S) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
rangeSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
RangeSum - Class in org.anchoranalysis.plugin.annotation.comparison
RangeSum() - Constructor for class org.anchoranalysis.plugin.annotation.comparison.RangeSum
rangeTimeIndex() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
rangeTPresent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
RasterArranger - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange
RasterArranger() - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.RasterArranger
rasterResizing() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
RasterTask<S,U> - Class in org.anchoranalysis.image.experiment.bean.task: An experiment that takes (primarily) a series of raster images as an input.
RasterTask() - Constructor for class org.anchoranalysis.image.experiment.bean.task.RasterTask
RasterWriterDelegateBase - Class in org.anchoranalysis.plugin.io.bean.stack.writer: A base class for a StackWriter delegates to another StackWriter based on values of a StackWriteOptions.
RasterWriterDelegateBase() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
ratioBounds() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
RatioFirstToSecond - Class in org.anchoranalysis.image.feature.bean.object.pair: Ratio of first-object to second-object in a pair
RatioFirstToSecond() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.RatioFirstToSecond
RatioNonMode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
RatioNonMode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
ratioPointsInsideRegion(Mark, List<Point3f>, RegionMap, int) - Static method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
RatioPrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: Calculates the ratio of prinicpal-axis length using Image Moments
RatioPrincipalAxisLength() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
RatioThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
RatioThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
read(Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationReader: Reads an annotation if it can, returns null otherwise
read(Path) - Method in class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationReader
read(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
ReadableTuple3i - Interface in org.anchoranalysis.spatial.point: Read-only access to a tuple
ReadAnnotationFromFile - Class in org.anchoranalysis.plugin.annotation.bean.strategy
readAssumeExists(Path) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.ReadAnnotationFromFile
readCheckExists(Path) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.ReadAnnotationFromFile
readDefaultMarks(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
readFile(Path) - Static method in class org.anchoranalysis.io.manifest.file.TextFileReader
readFromCSV(Path, boolean) - Static method in class org.anchoranalysis.image.experiment.label.FileLabelMap
readFromFile(Path) - Static method in class org.anchoranalysis.core.value.KeyValueParams
readMetadata(Path, boolean) - Static method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml: Looks for a metadata file describing the resolution
ReadOptions - Class in org.anchoranalysis.io.bioformats.bean.options
ReadOptions() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
ReadOptionsDelegate - Class in org.anchoranalysis.io.bioformats.bean.options: Forces a particular settings, but otherwise uses settings from a delegate
ReadOptionsDelegate() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
readResolutionXml(File) - Static method in class org.anchoranalysis.plugin.io.xml.ResolutionAsXml: Retrieves resolution from a XML file previously written by ResolutionAsXml.writeResolutionXml(Resolution, Path).
ReadVoxelExtentXml - Class in org.anchoranalysis.plugin.io.bean.stack.reader
ReadVoxelExtentXml() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
reconstruction(VoxelsWrapper, VoxelsWrapper, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction.GrayscaleReconstruction2DIJ
reconstruction(VoxelsWrapper, VoxelsWrapper, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionByErosion
reconstruction(VoxelsWrapper, VoxelsWrapper, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionRobinson
record(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
recordedOutputs() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: If defined, all output-names that are passed as arguments to both writers are recorded here.
RecordedOutputs - Class in org.anchoranalysis.io.output.recorded: Outputs recorded from RecordOutputNamesForWriter.
RecordedOutputs() - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputs
RecordedOutputsWithRules - Class in org.anchoranalysis.io.output.recorded: Rules to determine what outputting occurs, together with maybe an entity that records the output-names that are used when writing / querying.
RecordedOutputsWithRules() - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: Creates with no rules or outputs defined.
RecordedOutputsWithRules(MultiLevelRecordedOutputs, MultiLevelOutputEnabled, OutputEnabledDelta) - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: Creates with all elements defined.
recordError(Class<?>, String) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter: Reports an error that occurred as a string
recordError(Class<?>, String) - Method in class org.anchoranalysis.core.log.error.ErrorReporterIntoLog
recordError(Class<?>, String) - Method in class org.anchoranalysis.experiment.task.ErrorReporterForTask
recordError(Class<?>, Throwable) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter: Reports an error that occurred as an exception
recordError(Class<?>, Throwable) - Method in class org.anchoranalysis.core.log.error.ErrorReporterIntoLog
recordError(Class<?>, Throwable) - Method in class org.anchoranalysis.experiment.task.ErrorReporterForTask
RecordingWriters - Class in org.anchoranalysis.io.output.recorded: Two writers that record any output-names that are passed as arguments.
RecordingWriters(OutputterChecked, Optional<WriterExecuteBeforeEveryOperation>, Optional<MultiLevelRecordedOutputs>) - Constructor for class org.anchoranalysis.io.output.recorded.RecordingWriters: Creates the two writers.
recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in class org.anchoranalysis.io.manifest.operationrecorder.DualWriterOperationRecorder
recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in interface org.anchoranalysis.io.manifest.operationrecorder.WriteOperationRecorder: Records a subdirectory that has been recated.
recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.directory.JobRootDirectory
recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.directory.Subdirectory
recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.operationrecorder.DualWriterOperationRecorder
recordWrittenFile(String, ManifestDescription, Path, String) - Method in interface org.anchoranalysis.io.manifest.operationrecorder.WriteOperationRecorder: Records a file written.
RecursivelyDescribeExceptionStack - Class in org.anchoranalysis.core.exception.friendly: Generates a nice string representation of an Exception and its causes according to certain rules.
red() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
reduce() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Reduce the cost matrix by subtracting the smallest element of each row from all elements of the row as well as the smallest element of each column from all elements of the column.
reduce(List<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
reduce(List<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElements: Reduce a list of elements (each with a confidence score) to a smaller-list.
reduce(List<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
ReduceElements<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce: Reduces the number or spatial-extent of elements by favouring higher-confidence elements over lower-confidence elements.
ReduceElements() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElements
ReduceElementsGreedy<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce: Reduces the number or spatial-extent of elements by favouring higher-confidence elements over lower-confidence elements.
ReduceElementsGreedy() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
ReduceFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates the aggregate of a feature applied to both the first and second objects in a FeatureInputPairObjects.
ReduceFirstAndSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceFirstAndSecond
ReduceRatioFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates the aggregate of the ratio of first:second and second:first for a FeatureInputPairObjects
ReduceRatioFirstAndSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceRatioFirstAndSecond
Reference<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
Reference - Class in org.anchoranalysis.plugin.image.bean.channel.provider
Reference - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
Reference - Class in org.anchoranalysis.plugin.image.bean.mask.provider
Reference - Class in org.anchoranalysis.plugin.image.bean.object.provider
Reference - Class in org.anchoranalysis.plugin.image.bean.stack.provider
Reference - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
Reference - Class in org.anchoranalysis.plugin.points.bean.fitter
Reference() - Constructor for class org.anchoranalysis.feature.bean.operator.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
Reference() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.Reference
Reference(String) - Constructor for class org.anchoranalysis.feature.bean.operator.Reference
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Reference
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
Reference(String) - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
ReferencedFeatures<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
ReferencedFeatures() - Constructor for class org.anchoranalysis.feature.bean.list.ReferencedFeatures
ReferenceFactory - Class in org.anchoranalysis.plugin.image.provider: Creates reference (i.e.
ReferenceOrElse - Class in org.anchoranalysis.plugin.image.bean.object.provider: Returns a object-collection by name if it exists, or else calls objectsElse if it doesn't exist.
ReferenceOrElse() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
ReferenceOrEmpty - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection: Returns an existing marks-collection or an empty set if it doesn't exist
ReferenceOrEmpty() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
referenceString(Object) - Static method in class org.anchoranalysis.core.system.MemoryUtilities
ReflectInAxesWithinDistance - Class in org.anchoranalysis.plugin.points.bean.fitter: Reflects points in each axes if all points are within a certain distance from it
ReflectInAxesWithinDistance() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
reflectThroughOrigin() - Method in class org.anchoranalysis.spatial.box.BoundingBox: Reflects the bounding box through the origin (i.e.
RegEx - Class in org.anchoranalysis.bean.shared.regex: The regular-expression to use for matching groups.
RegEx() - Constructor for class org.anchoranalysis.bean.shared.regex.RegEx
RegExList - Class in org.anchoranalysis.bean.shared.regex
RegExList() - Constructor for class org.anchoranalysis.bean.shared.regex.RegExList
RegExMatcher - Class in org.anchoranalysis.plugin.io.bean.descriptivename
RegExMatcher() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
RegExpFilePathParser - Class in org.anchoranalysis.plugin.io.bean.groupfiles.parser
RegExpFilePathParser() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
RegExSimple - Class in org.anchoranalysis.bean.shared.regex
RegExSimple() - Constructor for class org.anchoranalysis.bean.shared.regex.RegExSimple
RegExSimple(String) - Constructor for class org.anchoranalysis.bean.shared.regex.RegExSimple
region() - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks: The region(s) of the marks that specifies the annotation.
region() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.core.mask.Mask
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A (sub-)region of the voxels.
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.extracter.Base
region(BoundingBox, boolean) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: A (sub-)region of the voxels.
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A (sub-)region of the object-mask.
regionIntersecting(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates an object-mask covering the a bounding-box (that is required to intersect at least partially)
regionIntersecting(BoundingBox, int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Like BoundedVoxels.region(org.anchoranalysis.spatial.box.BoundingBox, boolean) but only expects a bounding-box that intersects at least partially.
RegionMap - Class in org.anchoranalysis.mpp.bean.regionmap: Maps integer IDs to sub-regions in the map
RegionMap() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMap
RegionMap(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMap
RegionMapSingleton - Class in org.anchoranalysis.mpp.bean.regionmap
RegionMembership - Class in org.anchoranalysis.mpp.bean.regionmap
RegionMembership() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
RegionMembership(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
RegionMembershipAnd - Class in org.anchoranalysis.mpp.bean.regionmap
RegionMembershipAnd() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd
RegionMembershipAnd(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd
RegionMembershipOr - Class in org.anchoranalysis.mpp.bean.regionmap
RegionMembershipOr() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr
RegionMembershipUtilities - Class in org.anchoranalysis.mpp.bean.regionmap
RegionMembershipWithFlags - Class in org.anchoranalysis.mpp.bean.regionmap
RegionMembershipWithFlags(RegionMembership, int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
regionZ(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates an object-mask with a subrange of the slices.
regionZ(int, int, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Creates an box with a subrange of the slices.
register(String, AnchorBeanFactory) - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories: Registers a specific factory
register(String, CreateFromList<T>) - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories: Registers a bean that creates a List<>
registerAllPackageBeanFactories() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories: Registers the factories for the beans that exist in this package
registerBeanFactories() - Static method in class org.anchoranalysis.image.bean.RegisterBeanFactoriesImage
RegisterBeanFactories - Class in org.anchoranalysis.bean.xml: Utility class for registering the Bean-factories that are found in anchor-bean (or any other)
RegisterBeanFactoriesImage - Class in org.anchoranalysis.image.bean: Registers beans that needs particular factories
rejected() - Method in interface org.anchoranalysis.annotation.mark.DualMarks: The rejected marks.
RejectIfConditionXYResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader: If the XY resolution of an opened-image meets a certain condition then the resolution is scaled by a factor.
RejectIfConditionXYResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
RejectIfIntensityLessThan - Class in org.anchoranalysis.plugin.image.feature.bean.score
RejectIfIntensityLessThan() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
RejectIfNotConnected - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected: Rejects a set of objects, if any object is not fully connected (pixels form two or more separate connected components)
RejectIfNotConnected() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.RejectIfNotConnected
RejectIterationIfAllHigh - Class in org.anchoranalysis.image.voxel.object.morphological.accept
RejectIterationIfAllHigh() - Constructor for class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfAllHigh
RejectIterationIfLowDisconnected - Class in org.anchoranalysis.image.voxel.object.morphological.accept
RejectIterationIfLowDisconnected() - Constructor for class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfLowDisconnected
rejectProposal() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
relation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
relation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold: The relation to the threshold to consider
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
RelationBean - Class in org.anchoranalysis.bean.shared.relation
RelationBean() - Constructor for class org.anchoranalysis.bean.shared.relation.RelationBean
RelationToConstant - Class in org.anchoranalysis.bean.shared.relation.threshold
RelationToConstant() - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
RelationToConstant(RelationBean, double) - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
RelationToThreshold - Class in org.anchoranalysis.bean.shared.relation.threshold: A threshold and a relation to it, allowing for tests of a value in relation to a threshold.
RelationToThreshold() - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold
RelationToValue - Interface in org.anchoranalysis.math.relation
RelationWithMatches - Class in org.anchoranalysis.plugin.image.bean.object.filter.dependent: Matches each object with others, and keeps only those where a relation holds true for all matches (in terms of features)
RelationWithMatches() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
relativeMaskTo(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates a new object-mask with coordinates changed to be relative to another box.
relativePath() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
relativePath() - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
relativePath() - Method in class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
relativePositionTo(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBox: The relative position of the corner to another bounding box
relativePositionTo(Point3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.box.BoundingBox
relativePositionToBox(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBox: A new bounding-box using relative position coordinates to another box
relativeScale(Extent, Extent) - Static method in class org.anchoranalysis.spatial.scale.ScaleFactorUtilities: Calculates a scaling factor so as to scale sdSource to sdTarget
releaseKeepBest() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
releaseKeepBest() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
remove() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
remove(int) - Method in class org.anchoranalysis.core.color.ColorList
remove(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
remove(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
remove(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
remove(int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
remove(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
remove(int) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
remove(int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
remove(int) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
remove(int) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
remove(int, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
remove(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
remove(EnergySavedInd, int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
remove(MemoCollection, int, VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
remove(MemoCollection, VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
remove(MemoForIndex, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
remove(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
remove(VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
removeAll(Collection<?>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
removeAndUpdateEnergy(VoxelizedMarksWithEnergy, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelDeathPixelized
removeAndUpdateEnergy(MarksFromPartition, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelDeathPartition
removeAndUpdateEnergy(T, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
removeBelowThreshold(int) - Method in class org.anchoranalysis.math.histogram.Histogram
removeClosestToUnitZ() - Method in class org.anchoranalysis.math.moment.ImageMoments
removeEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Remove an edge between two vertices.
removeEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Remove an edge between two vertices.
RemoveExtensions - Class in org.anchoranalysis.plugin.io.bean.descriptivename: Removes extensions from the descriptive-name (but not from the file) AND only if the extension hasn't already been removed upstream.
RemoveExtensions() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
RemoveExtensions(FileNamer) - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
removeIfExists(FeatureList<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
removeIfExists(T) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
removeIntersectingVoxels(ObjectCollection, Dimensions, boolean) - Static method in class org.anchoranalysis.plugin.image.object.ObjectIntersectionRemover
RemoveIntersectingVoxels - Class in org.anchoranalysis.plugin.image.bean.object.provider.split: Considers all possible pairs of objects in a provider, and removes any intersecting pixels
RemoveIntersectingVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
removeLeft(int) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath: Removes the first numToRemove pixels from the left
RemoveMatching - Class in org.anchoranalysis.plugin.io.bean.provider.file
RemoveMatching() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching
removeNonMatching(List<T>) - Method in class org.anchoranalysis.plugin.io.input.filter.FilterDescriptiveNameEqualsContains
removeOrReplace(boolean, boolean, boolean) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate: Chops of one-side of keep, and one-side of merge
RemoveOverlappingBoundingBoxes - Class in org.anchoranalysis.plugin.image.bean.box: Non-maxima suppression for axis-aligned bounding-boxes using an Intersection over Union score.
RemoveOverlappingBoundingBoxes() - Constructor for class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes
RemoveOverlappingObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce: Non-maxima suppression for object-masks using an Intersection over Union score.
RemoveOverlappingObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
RemovePartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
RemovePartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartition
RemovePartitionAndThen<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
RemovePartitionAndThen() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
removePointsInMark(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
removeRight(int) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath: Removes the last numToRemove pixels from the right
RemoveTouchingBorder - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter: Considers all possible pairs of objects in a provider, and removes those that touch the border.
RemoveTouchingBorder() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
removeTouchingBorderXY(Extent) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
RemoveTrailingDirectory - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive
RemoveTrailingDirectory() - Constructor for class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
removeTwo(int, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
removeTwo(int, int, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
removeTwo(EnergySavedInd, int, int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
removeTwo(MemoCollection, int, int, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
removeVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload: Removes a vertex and any edges connected to it.
removeVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Removes a vertex and any edges connected to it.
RemoveWhitespace - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming: Removes any whitespace characters from the path
RemoveWhitespace() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.RemoveWhitespace
repeat(int, CheckedRunnable<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Repeats an operation a number of times.
Repeat - Class in org.anchoranalysis.bean.shared.color.scheme
Repeat - Class in org.anchoranalysis.plugin.image.bean.segment.binary
Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position
Repeat() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Repeat
Repeat() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
Repeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
Repeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
Repeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice: Creates a new channel with specific dimensions that repeatedly duplicates a slice from an existing channel
RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice: Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing mask
RepeatSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
RepeatSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
repeatUntil(int, CheckedBooleanSupplier<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Repeats an operation until a true value is returned.
repeatWithIndex(int, CheckedIntConsumer<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Repeats an operation a number of times, passing an increment index to operation each time.
Replace - Class in org.anchoranalysis.plugin.io.bean.path.derive: Generates a file-path by replacing all occurrences of a string-pattern with another
Replace() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Replace
replaceBy(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.core.mask.Mask
replaceError(ErrorNode) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
replaceError(ErrorNode) - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
replaceError(ErrorNode) - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
ReplaceInfinity<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
ReplaceInfinity() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceInfinity
replaceInput(T) - Method in class org.anchoranalysis.feature.session.SessionInputSequential: Replaces existing input with new input
replaceInputManager(InputManager<?>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
replaceInputManager(InputManager<?>) - Method in interface org.anchoranalysis.experiment.io.ReplaceInputManager
replaceInputManager(InputManager<?>) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
replaceInputManager(InputManager<?>) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
ReplaceInputManager - Interface in org.anchoranalysis.experiment.io: Indicates and provides a mechanism that the InputManager can be replaced.
ReplaceNaN<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
ReplaceNaN() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceNaN
replaceOutputManager(OutputManager) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
replaceOutputManager(OutputManager) - Method in interface org.anchoranalysis.experiment.io.ReplaceOutputManager
replaceOutputManager(OutputManager) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
replaceOutputManager(OutputManager) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
ReplaceOutputManager - Interface in org.anchoranalysis.experiment.io: Indicates and provides a mechanism that the OutputManager can be replaced.
ReplacePropertyBeanFactory<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.xml.factory: Replaces a property (an XML element of attribute) on a bean before loading it
ReplacePropertyBeanFactory(BeanInstanceMap) - Constructor for class org.anchoranalysis.bean.xml.factory.ReplacePropertyBeanFactory
replaceSlice(int, VoxelBuffer<FloatBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
replaceSlice(int, VoxelBuffer<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
replaceSlice(int, VoxelBuffer<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
replaceSlice(int, VoxelBuffer<UnsignedShortBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
replaceSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
replaceSlice(int, VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
replaceSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.Voxels: Assigns a new buffer for a slice
ReplaceStrategy<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.strategy.replace
replaceTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
replaceTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
replaceTask(Task<T, S>) - Method in interface org.anchoranalysis.experiment.io.ReplaceTask
replaceTask(Task<U, S>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
ReplaceTask<T extends InputFromManager,S> - Interface in org.anchoranalysis.experiment.io: /** Indicates and provides a mechanism that the Task can be replaced.
ReplaceUnusualValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace: Calculates the underlying feature, but replaces the result with a constant if it happens to be an "unusual" value
ReplaceUnusualValue() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
replaceVoxels(Voxels<?>) - Method in class org.anchoranalysis.image.core.channel.Channel: Assigns new voxels to replace the existing voxels
replaceVoxels(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Replaces the voxels in the object-mask.
replaceVoxels(Voxels<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Replaces the voxels in the box.
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
reportBegin(FeedbackBeginParameters<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
reportEnd(FeedbackEndParameters<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
ReporterAggregate<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
ReporterAggregate() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
ReporterAggregate(double) - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
ReporterException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback
ReporterException(String) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.ReporterException
ReporterException(Throwable) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.ReporterException
ReporterInterval<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
ReporterInterval() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
ReporterInterval(double) - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
ReportFeature<T> - Class in org.anchoranalysis.io.output.bean
ReportFeature() - Constructor for class org.anchoranalysis.io.output.bean.ReportFeature
ReportFeatureEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
ReportFeatureEvaluator() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
ReportFeatureForManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
ReportFeatureForManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifest
ReportFeatureForManifestFileBase - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
ReportFeatureForManifestFileBase() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
ReportFeatureForMPP<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
ReportFeatureForMPP() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
ReportFeatureForSharedObjects - Class in org.anchoranalysis.mpp.io.bean.report.feature
ReportFeatureForSharedObjects() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForSharedObjects
ReportFeatureOnMark - Class in org.anchoranalysis.mpp.io.bean.report.feature
ReportFeatureOnMark() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
ReportFeatureOnMarks - Class in org.anchoranalysis.mpp.io.bean.report.feature
ReportFeatureOnMarks() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
ReportFeatureOnObject - Class in org.anchoranalysis.mpp.io.bean.report.feature
ReportFeatureOnObject() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObject
ReportFeatureOnObjectCollection - Class in org.anchoranalysis.mpp.io.bean.report.feature
ReportFeatureOnObjectCollection() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectCollection
ReportFeatureOnObjectsBase<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
ReportFeatureOnObjectsBase() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
ReportFeatureWrapError - Class in org.anchoranalysis.mpp.io.bean.report.feature
ReportFeatureWrapError() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
reporting(int, StateReporter<T, U>, TransformationContext) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
Reporting<S> - Class in org.anchoranalysis.mpp.segment.optimization.step: Exposes data which is only needed by reporting tools
reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
reportItr(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
reportItr(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
reportItr(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
reportItr(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
reportItr(Reporting<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.KernelIterDescriptionSerializerPeriodicReporter
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
reportNewBest(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
reportNewBest(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
reportNewBest(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
reportNewBest(Reporting<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
RequireArguments - Class in org.anchoranalysis.experiment.bean.require
RequireArguments() - Constructor for class org.anchoranalysis.experiment.bean.require.RequireArguments
RequireDebugMode - Class in org.anchoranalysis.experiment.bean.require
RequireDebugMode() - Constructor for class org.anchoranalysis.experiment.bean.require.RequireDebugMode
RequireFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
RequireFeatureRelationThreshold() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
reset() - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
reset() - Method in class org.anchoranalysis.math.arithmetic.RunningSum: Reset the sum and count to zero
reset() - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection: Resets all items to zero.
reset() - Method in class org.anchoranalysis.math.histogram.Histogram
reset() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
reset() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
reset() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
reset() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
resetInd() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
ResettableCalculation - Interface in org.anchoranalysis.feature.calculate.cache: A calculation that be invalidated (resetted), removing any existing cached value.
resizedXY(int, int, Interpolator) - Method in class org.anchoranalysis.image.voxel.extracter.Base
resizedXY(int, int, Interpolator) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Creates a new voxels that are a resized version of the current voxels (only in X and Y dimensions), interpolating as needed.
resizeXY(int, int) - Method in class org.anchoranalysis.image.core.channel.Channel
resizeXY(int, int, Interpolator) - Method in class org.anchoranalysis.image.core.channel.Channel
resizeXY(Extent) - Method in class org.anchoranalysis.image.core.channel.Channel
resizeXY(Extent, Interpolator) - Method in class org.anchoranalysis.image.core.channel.Channel
resolution() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The image-resolution asssociated with the energy-stack.
resolution() - Method in class org.anchoranalysis.image.core.channel.Channel
resolution() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Resolution of voxels to physical measurements e.g.
resolution() - Method in class org.anchoranalysis.image.core.mask.Mask
resolution() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
resolution() - Method in class org.anchoranalysis.image.core.stack.Stack
Resolution - Class in org.anchoranalysis.image.core.dimensions: The resolution of an image.
Resolution() - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution
Resolution(double, double, double) - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution
Resolution(Tuple3d) - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution: Constructs a resolution from a tuple.
ResolutionAsXml - Class in org.anchoranalysis.plugin.io.xml: Reads and writes a metadata XML file specifying the image-resolution.
resolutionRequired() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
resolve(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.Bound
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
resolve(Optional<UnitConverter>, Point3d, Point3d) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
resolve(Optional<UnitConverter>, Point3i, Point3i) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
resolveArea(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
resolveArea(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter: Convert area into another unit representation
ResolvedBound - Class in org.anchoranalysis.mpp.bean.bound: A bound resolved into pixel units
ResolvedBound() - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
ResolvedBound(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
ResolvedBound(ResolvedBound) - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
ResolvedCalculation<S,T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.cache: Like a FeatureCalculation but has been resolved against a cache to reuse any existing identical instance.
ResolvedCalculation(FeatureCalculation<S, T>) - Constructor for class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation
ResolvedCalculationMap<S,T extends FeatureInput,U> - Class in org.anchoranalysis.feature.calculate.cache: A FeatureCalculationMap that has been resolved against a cache.
ResolvedCalculationMap(FeatureCalculationMap<S, T, U, FeatureCalculationException>) - Constructor for class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap: Constructor
resolveDistance(double, Optional<Resolution>, DirectionVector) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter: Convert distance into another unit representation
resolveFeatureIdentifier(String) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSymbolCalculator: Due to scoping (different prefixes that can exist), an ID needs to be resolved to a unique-string before it can be passed to calculateFeatureByIdentifier
resolveForAxis(Optional<UnitConverter>, AxisType) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance: Resolves the distance in a direction aligned to a particular axis
resolveName(String) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean: Adds a prefix before the name
resolvePath(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: An absolute path to the prefix
resolvePath(Path) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: Converts a relative-path to an absolute-path (relative to the file-path associated with this current bean)
resolvePathToCurrentJar(String) - Method in class org.anchoranalysis.launcher.FilePathResolver
resolvePathToCurrentJar(Path) - Method in class org.anchoranalysis.launcher.FilePathResolver
resolver() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput: Returns a resolver for calculations
resolver() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
resolveTestPath(String) - Method in class org.anchoranalysis.test.TestLoader: Resolves a path to test-data (relative path to the test-data root) to an absolute path on the file system
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.UnitValueAreaOrVolume: Resolves a measurement of area/volume (in whatever units) to units corresponding to the image pixels/voxels.
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
resolveVolume(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
resolveVolume(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter: Convert volume into another unit representation
resources() - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Config for resources sued by the launcher
ResourcesConfig - Class in org.anchoranalysis.launcher.config
ResourcesConfig(ClassLoader, String, String, String, String) - Constructor for class org.anchoranalysis.launcher.config.ResourcesConfig
ResultsVector - Class in org.anchoranalysis.feature.results: A vector of results from feature-calculations.
ResultsVector(int) - Constructor for class org.anchoranalysis.feature.results.ResultsVector
ResultsVectorList - Class in org.anchoranalysis.feature.results: A list of elements of type ResultsVector.
ResultsVectorList() - Constructor for class org.anchoranalysis.feature.results.ResultsVectorList
ResultsVectorList(ResultsVector) - Constructor for class org.anchoranalysis.feature.results.ResultsVectorList
ResultsVectorTestUtilities - Class in org.anchoranalysis.test.feature.plugins
ResultsVectorWithThumbnail - Class in org.anchoranalysis.plugin.image.task.feature: A results-vector with an optional thumbnail associated with it
ResultsVectorWithThumbnail(ResultsVector) - Constructor for class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
ResultsVectorWithThumbnail(ResultsVector, Optional<DisplayStack>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
ResultsWriter - Class in org.anchoranalysis.feature.io.results: Feature calculation results that can be outputted in different ways.
ResultsWriter(ResultsWriterMetadata, InputOutputContext) - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriter: Creates for metadata and in a particular directory.
ResultsWriterMetadata - Class in org.anchoranalysis.feature.io.results: Additional information needed for the outputs in ResultsWriter.
ResultsWriterMetadata(LabelHeaders, FeatureNameList, ResultsWriterOutputNames) - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriterMetadata
ResultsWriterOutputNames - Class in org.anchoranalysis.feature.io.results: The customizable output names used by ResultsWriter, which all follow a pattern based on a prefix.
ResultsWriterOutputNames() - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames: Creates using default names, equivalent to a prefix of features.
ResultsWriterOutputNames(String, boolean, boolean) - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames: Creates output-names based upon a prefix.
retainAll(Collection<?>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
RetrieveDestinationFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
RetrieveDestinationFromDual() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveDestinationFromDual
RetrieveDestinationFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
RetrieveDestinationFromVoxelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveDestinationFromVoxelized
RetrieveSingleMarkOnly - Class in org.anchoranalysis.plugin.mpp.bean.provider.single: Retrieves a mark from a marks, assuming there is only one mark in a marks, otherwise throwing an exception
RetrieveSingleMarkOnly() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
RetrieveSourceFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
RetrieveSourceFromDual() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveSourceFromDual
RetrieveSourceFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
RetrieveSourceFromVoxelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveSourceFromVoxelized
reuseByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Like BinaryVoxelsFactory.reuseByte(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>) but uses default binary-values for OFF (0) and ON (255).
reuseByte(Voxels<UnsignedByteBuffer>, BinaryValues) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have only two intensity-values representing OFF and ON
reuseInt(Voxels<UnsignedIntBuffer>, BinaryValues) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Reuses an existing voxel-buffer (of type unsigned int) as a binary-version which should have only two intensity-values representing OFF and ON
ReuseSingletonStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.replace: Always re-use a singleton SessionInput, invalidating it each time a new call occurs
ReuseSingletonStrategy(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.ReuseSingletonStrategy: Constructor with default means of creating a session-input
ReuseSingletonStrategy(CacheCreator, FindChildStrategy) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.ReuseSingletonStrategy: Constructor with custom means of creating a session-input
reverse() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
reversedList(List<Point3i>) - Static method in class org.anchoranalysis.image.core.outline.traverser.visited.ReverseUtilities
reverseIterateArray(T[], CheckedConsumer<T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate: Iterates through every element in an array in reverse order
ReverseUtilities - Class in org.anchoranalysis.image.core.outline.traverser.visited
rewind() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Rewinds the buffer ala ByteBuffer.rewind().
RGB - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Converts a set of channels to a single RGB-stack.
RGB() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB
rgbColor() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
RGBColor - Class in org.anchoranalysis.core.color
RGBColor() - Constructor for class org.anchoranalysis.core.color.RGBColor
RGBColor(int) - Constructor for class org.anchoranalysis.core.color.RGBColor
RGBColor(int, int, int) - Constructor for class org.anchoranalysis.core.color.RGBColor
RGBColor(Color) - Constructor for class org.anchoranalysis.core.color.RGBColor
RGBColorBean - Class in org.anchoranalysis.bean.shared.color
RGBColorBean() - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
RGBColorBean(int, int, int) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
RGBColorBean(Color) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
RGBColorBean(RGBColor) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
RGBOutputUtils - Class in org.anchoranalysis.image.core.stack.rgb
RGBStack - Class in org.anchoranalysis.image.core.stack.rgb: A stack with exactly three channels, respectively for Red, Green and Blue colors.
RGBStack(Channel, Channel, Channel) - Constructor for class org.anchoranalysis.image.core.stack.rgb.RGBStack
RGBStack(Dimensions, ChannelFactorySingleType) - Constructor for class org.anchoranalysis.image.core.stack.rgb.RGBStack: Creates a particularly-sized stack with all channels initialized to 0.
RGBStack(Stack) - Constructor for class org.anchoranalysis.image.core.stack.rgb.RGBStack: Creates from an existing stack (which must have 1 or 3 channels).
rightSize() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
rmv(int) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
rmvFromUpdatablePairList(ListUpdatableMarkSetCollection, Mark) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
RootDirectory - Class in org.anchoranalysis.io.manifest.directory
RootDirectory(Path) - Constructor for class org.anchoranalysis.io.manifest.directory.RootDirectory
Rooted - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer: Prepend a 'root' before the file-path-prefix obtained from a delegate
Rooted - Class in org.anchoranalysis.plugin.io.bean.path.derive
Rooted - Class in org.anchoranalysis.plugin.io.bean.provider.file: Represents a set of files, with a different root depending on the operating-system and conditions.
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
RootedFilePath - Class in org.anchoranalysis.plugin.io.bean.filepath
RootedFilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
RootedFilePathUtilities - Class in org.anchoranalysis.plugin.io.input.path
RootFilePathRegEx - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
RootFilePathRegEx() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer: Provides a prefix that becomes the root-folder.
rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
rootFolderPrefixAvoidResolve(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: Provides a prefix that becomes the root-folder.
RootPath - Class in org.anchoranalysis.bean.shared.path: Defines a *root path* i.e.
RootPath() - Constructor for class org.anchoranalysis.bean.shared.path.RootPath
RootPathMap - Class in org.anchoranalysis.plugin.io.input.path: A collection of root-paths indexed by their name.
RotatableBoundingBox - Class in org.anchoranalysis.mpp.mark.points: A two-dimensional bounding-box rotated at arbitrary angle in XY plane around a point.
RotatableBoundingBox() - Constructor for class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
rotate(double) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
RotateAngle2D - Class in org.anchoranalysis.spatial.rotation.factory
RotateAngle2D(double) - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotateAngle2D
RotateAngle3D - Class in org.anchoranalysis.spatial.rotation.factory
RotateAngle3D(double, double, double) - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotateAngle3D
RotateAxisAngle - Class in org.anchoranalysis.spatial.rotation.factory
RotateAxisAngle(Vector3d, double) - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotateAxisAngle
rotatedPoint(double[]) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
rotatedPoint(Point3d) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
rotateOneVectorOntoAnother(Vector3d, Vector3d) - Static method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
RotationBounds - Class in org.anchoranalysis.mpp.bean.mark.bounds
RotationBounds() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds
RotationBounds2D - Class in org.anchoranalysis.mpp.bean.mark.bounds: Creates a randomly-generated orientation in 2D by uniformally sampling a scalar rotation angle
RotationBounds2D() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
RotationBounds3D - Class in org.anchoranalysis.mpp.bean.mark.bounds: Creates a randomly-generated orientation in 3D based upon Euler Angles
RotationBounds3D() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
RotationMatrix - Class in org.anchoranalysis.spatial.rotation: A matrix that performs a rotation in Euclidean space.
RotationMatrix(int) - Constructor for class org.anchoranalysis.spatial.rotation.RotationMatrix
RotationMatrix(DoubleMatrix2D) - Constructor for class org.anchoranalysis.spatial.rotation.RotationMatrix
RotationMatrixFactory - Class in org.anchoranalysis.spatial.rotation.factory: Base for classes that create a RotationMatrix in different ways.
RotationMatrixFactory() - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory
RowLabels - Class in org.anchoranalysis.feature.io.csv: Labels for each row of feature-results in the outputted CSV row.
RowLabels(String) - Constructor for class org.anchoranalysis.feature.io.csv.RowLabels: Creates with a single string as an identifier.
RowLabels(Optional<String[]>, Optional<MultiName>) - Constructor for class org.anchoranalysis.feature.io.csv.RowLabels
RTree<T> - Class in org.anchoranalysis.spatial.rtree: An R-Tree that contains items, each with an associated bounding-box.
RTree(int) - Constructor for class org.anchoranalysis.spatial.rtree.RTree: Creates an empty R-Tree.
run() - Method in interface org.anchoranalysis.core.functional.checked.CheckedRunnable
runCommandLineApp(String[], LauncherConfig, Logger) - Static method in class org.anchoranalysis.launcher.Launch: Runs a command-line app, by parsing arguments
runExperiment(String) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell: Runs an experiment identified by an XML found in the resources
runExperiment(String, Optional<String>, Optional<String>) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell: Runs an experiment identified by an XML found in the resources
runExperimentInTemporaryFolder(String, Optional<String>, Optional<String>, TemporaryFolder, String[]) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell: Creates a temporary-folder, copies data all data from the associated test-loader, and runs an experiment
runExperimentInTemporaryFolder(String, TemporaryFolder) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell: Creates a temporary-folder, copies data all data from the associated test-loader, and runs an experiment
RunningSum - Class in org.anchoranalysis.math.arithmetic: Mutable class that allows for incrementing jointly sum and count variables, so as to eventually calculate the mean.
RunningSum() - Constructor for class org.anchoranalysis.math.arithmetic.RunningSum
RunningSum(double, long) - Constructor for class org.anchoranalysis.math.arithmetic.RunningSum
RunningSumCollection - Class in org.anchoranalysis.math.arithmetic: A collection of RunningSum where an operation is executed on all objects in the collection.
RunningSumCollection(int) - Constructor for class org.anchoranalysis.math.arithmetic.RunningSumCollection: Constructor.
RunningSumPoint - Class in org.anchoranalysis.spatial.point: A running sum for tracking points in each dimension
RunningSumPoint() - Constructor for class org.anchoranalysis.spatial.point.RunningSumPoint

S

sample(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
sample(RandomNumberGenerator) - Method in interface org.anchoranalysis.mpp.probmap.PointSampler
sample(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.probmap.ProbMapObjects
sample(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
sampleDoubleFromRange(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a uniformly random floating-point number within a range from 0 (exclusive) to endExclusive.
sampleDoubleFromRange(double, double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a uniformly random floating-point number within a range.
sampleDoubleFromZeroCenteredRange(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a uniformly random floating-point number centered around 0 ranging from [-halfWidth,+halfWidth] (both exclusive).
sampleDoubleZeroAndOne() - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Samples from a uniformly-distributed range between 0.0 (exclusive) and 1.0 (exclusive).
sampleDoubleZeroAndOne() - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
sampleFromAvailable(int) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks: Samples from the available marks
sampleFromList(List<T>) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Samples uniformly an item from a list
sampleInteger(int) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Samples an integer uniformally between [0..maxVal)
sampleIntFromRange(int) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a uniformly random discrete number within a range from 0 (inclusive) to endExclusive.
sampleIntFromRange(int, int) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Samples from a uniformly random discrete number within a range.
sampleLongFromRange(long) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator: Generates a uniformly random discrete number within a range from 0 (inclusive) to endExclusive.
sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.pair.RandomCollection
SampleWithDirectory - Class in org.anchoranalysis.plugin.io.bean.provider.file
SampleWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
ScalarProposer - Class in org.anchoranalysis.mpp.bean.proposer
ScalarProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.ScalarProposer
ScalarThreeDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer: Like a IntConsumer but accepts three coordinates of a point as scalar arguments.
ScalarTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer: Like a IntConsumer but accepts two coordinates of a point as scalar arguments.
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.Bound
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
scale(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
scale(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
scale(double) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Objects are scaled in pre-rotated position.
scale(double) - Method in class org.anchoranalysis.mpp.mark.Mark: Scales the mark in X and Y dimensions.
scale(double) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
scale(double) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
scale(double) - Method in class org.anchoranalysis.mpp.mark.points.PointList
scale(double) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
scale(double) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
scale(double) - Method in class org.anchoranalysis.spatial.point.Point2d
scale(double) - Method in class org.anchoranalysis.spatial.point.Point2f
scale(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
scale(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
scale(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
scale(Channel, ScaleCalculator, Interpolator, MessageLogger) - Static method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
scale(Mask, ScaleCalculator) - Static method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
scale(ScaleFactor) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Produces a scaled-version of an object-mask.
scale(ScaleFactor) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Scales the bounding-box, both the corner-point and the extent
scale(ScaleFactor, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Produces a scaled-version of an object-mask.
scale(ScaleFactor, Interpolator, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Creates a scaled-version (in XY dimensions only) of the current bounding-box
scale(ScaleFactor, Extent) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects: Scales the segmented-objects.
scale(ScaleFactor, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Scales the bounding-box corner-point, and assigns a new extent
scale(ScaleFactor, Point3i) - Static method in class org.anchoranalysis.spatial.scale.ScaleFactorUtilities: Scales a point in XY (immutably)
Scale - Class in org.anchoranalysis.plugin.image.bean.object.provider: Scales all the objects in the collection by a particular scale-factor.
Scale - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
Scale() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Scale
Scale() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
scaleBy(double) - Method in class org.anchoranalysis.math.histogram.Histogram
ScaleByMinMaxValue - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Scales by compressing a certain range of values into the 8-bit signal
ScaleByMinMaxValue() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
ScaleByParams - Class in org.anchoranalysis.plugin.image.bean.channel.convert: Scales by compressing a certain range of values into the 8-bit signal
ScaleByParams() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
ScaleByTypeToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert
ScaleByTypeToByte() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByTypeToByte
ScaleCalculator - Class in org.anchoranalysis.image.bean.spatial
ScaleCalculator() - Constructor for class org.anchoranalysis.image.bean.spatial.ScaleCalculator
ScaleCalculatorConstant - Class in org.anchoranalysis.plugin.image.bean.scale
ScaleCalculatorConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
ScaleCalculatorInverted - Class in org.anchoranalysis.plugin.image.bean.scale
ScaleCalculatorInverted() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
ScaleCalculatorMinXYRes - Class in org.anchoranalysis.plugin.image.bean.scale
ScaleCalculatorMinXYRes() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
ScaleCalculatorRelativeDimensions - Class in org.anchoranalysis.plugin.image.bean.scale
ScaleCalculatorRelativeDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
scaleClipTo(ScaleFactor, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Scales the bounding-box, both the corner-point and the extent - ensuring it remains inside a containing-extent
ScaledElements<T> - Class in org.anchoranalysis.image.core.object.scale: A list of elements with an object-mask representation that have been scaled.
ScaledMaskCreator - Interface in org.anchoranalysis.overlay.object.scaled: Creates a scaled version of a mask from a mark/object that is not scaled
scaledObjectFor(T) - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements: Gets the scaled version of an element given the unscaled element.
scaleElements(List<T>, ScaleFactor, Extent, AccessObjectMask<T>) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler: Scales every element in a list collectively, ensuring the results remain inside a particular region.
ScaleFactor - Class in org.anchoranalysis.spatial.scale: What to scale x and y dimensions by
ScaleFactor(double) - Constructor for class org.anchoranalysis.spatial.scale.ScaleFactor
ScaleFactor(double, double) - Constructor for class org.anchoranalysis.spatial.scale.ScaleFactor
ScaleFactorUtilities - Class in org.anchoranalysis.spatial.scale
ScaleImage - Class in org.anchoranalysis.plugin.image.task.bean.scale: Task to scale an image.
ScaleImage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
scaleObjects(ObjectCollection, ScaleFactor) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler: Scales every object-mask in a collection
scaleObjects(ObjectCollection, ScaleFactor, Optional<UnaryOperator<ObjectMask>>, Optional<UnaryOperator<ObjectMask>>) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler: Scales every object-mask in a collection, allowing for additional manipulation before and after scaling.
scaleObjects(ObjectCollection, ScaleFactor, Extent) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler: Scales every object-mask in a collection, ensuring the results remain inside a particular region.
scaleQuantity(double, int) - Static method in class org.anchoranalysis.spatial.scale.ScaleFactorUtilities: Multiplies a quantity (integer) by a scaling-factor, returning it as an integer
Scaler - Class in org.anchoranalysis.image.core.object.scale: Scales object-masks (or other more generic elements) collectively to avoid undesired overlap.
scaleRadii(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
ScaleToSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack: Create a thumbnail by scales an image to a particular size.
ScaleToSize() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
scaleX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
scaleXY(double) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation: Scales the marks in the annotation in X and Y dimensions.
scaleXY(double) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
scaleXY(double) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Scales the mark in X and Y dimensions.
scaleXY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
scaleXY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
scaleXY(double, Extent) - Method in interface org.anchoranalysis.image.core.object.seed.Seed
scaleXY(double, Extent) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
scaleXY(double, Extent) - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
scaleXY(ScaleFactor) - Method in class org.anchoranalysis.image.core.channel.Channel
scaleXY(ScaleFactor) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
scaleXY(ScaleFactor) - Method in class org.anchoranalysis.image.core.mask.Mask
scaleXY(ScaleFactor, Interpolator) - Method in class org.anchoranalysis.image.core.channel.Channel
ScaleXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity: Scales the channel in the X and Y dimensions.
ScaleXY - Class in org.anchoranalysis.plugin.image.bean.mask.provider.resize: Scales the mask in XY dimensions, but not in Z dimension.
ScaleXY - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
ScaleXY() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
ScaleXY() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
ScaleXY() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
scaleXYBy(ScaleFactor) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
scaleXYBy(ScaleFactor) - Method in class org.anchoranalysis.spatial.Extent
scaleXYPoint(Point3d, double) - Static method in class org.anchoranalysis.mpp.mark.MarkWithPosition
scaleXYTo(int, int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
scaleY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
sceneContains(Point2i) - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture
ScoreObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
ScoreObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
ScoreVoxels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score: Assigns a score (a value indicating how probable something is) to each voxel
ScoreVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
search(FeatureCalculation<S, T>) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculationResolver: Searches for an equivalent calculation to calculation
search(FeatureCalculationMap<S, T, U, FeatureCalculationException>) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculationResolver: Searches for an equivalent calculation to calculation
second(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
second(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
second(String) - Method in interface org.anchoranalysis.io.output.enabled.multi.MultiLevelOutputEnabled: A second-level of OutputEnabled for a particular outputName as used in first-level.
second(String) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
second(String) - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: A RecordedOutputs for recording second-level outputs for a given outputName from the first-level.
Second - Class in org.anchoranalysis.image.feature.bean.object.pair: Evaluates the first-object in a pair only
Second() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Second
Second(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Second
SECOND - org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
secondaryReport() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.StateReporter
secondaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterIdentity
secondaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
secondaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
secondEntries() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs: All second-level recorded output entries.
secondLevel(String) - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.
secondLevelOutputs(String, OutputEnabled) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
secondPart() - Method in class org.anchoranalysis.feature.io.name.CombinedName
secondPart() - Method in interface org.anchoranalysis.feature.io.name.MultiName: The second part of the name.
secondPart() - Method in class org.anchoranalysis.feature.io.name.SimpleName
Seed - Interface in org.anchoranalysis.image.core.object.seed: A seed provides an voxels that exclusively belong to a particular object, and can be used as a starting hint for segmentation.
SeedCollection - Class in org.anchoranalysis.image.core.object.seed
SeedCollection() - Constructor for class org.anchoranalysis.image.core.object.seed.SeedCollection
SeedFinderException - Exception in org.anchoranalysis.image.experiment.seed
SeedFinderException(String) - Constructor for exception org.anchoranalysis.image.experiment.seed.SeedFinderException
SeedFinderException(Throwable) - Constructor for exception org.anchoranalysis.image.experiment.seed.SeedFinderException
SeedObjectMask - Class in org.anchoranalysis.image.core.object.seed
SeedObjectMask(ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.seed.SeedObjectMask
seek(int) - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: Seeks a particular slice
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects: Segments a channel to produce an object-collection.
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
segment(NamedStacks, NamedProvider<ObjectCollection>, Optional<KeyValueParams>, InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
segment(NamedStacks, NamedProvider<ObjectCollection>, Optional<KeyValueParams>, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
segment(Stack) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled: Segments individually using a pool of size 1 just for one stack
segment(Stack, ConcurrentModelPool<Net>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
segment(Stack, ConcurrentModelPool<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled: Segments a stack to produce an object-collection.
segment(Stack, ConcurrentModelPool<T>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentation: Performs a segmentation on voxels so that each voxel has an ON or OFF state after the operation.
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderMask
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderWithoutMask
SegmentationBean<T> - Class in org.anchoranalysis.image.bean.segment: Performs some kind of segmentation
SegmentationBean() - Constructor for class org.anchoranalysis.image.bean.segment.SegmentationBean
SegmentationFailedException - Exception in org.anchoranalysis.image.bean.nonbean.error
SegmentationFailedException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.SegmentationFailedException
SegmentationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.SegmentationFailedException
SegmentationFailedException(Throwable) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.SegmentationFailedException
SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment: Applies a BinarySegmentation algorithm to derive a mask from a channel
SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
SegmentChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
SegmentChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
SegmentChannelByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Performs segmentation of a channel using each object in the upstream collection as a mask.
SegmentChannelByObject() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
SegmentChannelIntoObjects - Class in org.anchoranalysis.image.bean.segment.object: A base class for algorithms to segment a channel into one or more objects.
SegmentChannelIntoObjects() - Constructor for class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
SegmentChannelIntoObjectsUnary - Class in org.anchoranalysis.image.bean.segment.object: A base-class for segmentations that takes another object-segmentation algorithm as a parameter.
SegmentChannelIntoObjectsUnary() - Constructor for class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
SegmentedObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.stack: Objects that are a result of an instance-segmentation.
SegmentedObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
SegmentedObjects(List<WithConfidence<ObjectMask>>) - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Invert
segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
SegmentInstanceWithModel<T> - Class in org.anchoranalysis.plugin.image.task.bean.segment: Using a model-pool, performs instance segmentation on an image producing zero, one or more objects per image.
SegmentInstanceWithModel() - Constructor for class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
SegmentIntoMarks - Class in org.anchoranalysis.mpp.segment.bean
SegmentIntoMarks() - Constructor for class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
SegmentMarksFromImage - Class in org.anchoranalysis.plugin.mpp.experiment.bean.segment: Segments an image into a collection of Marks.
SegmentMarksFromImage() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
SegmentOnMaximumIntensityAndExpandInZ - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel: Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D segmentation.
SegmentOnMaximumIntensityAndExpandInZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
SegmentStack<T> - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Segments a stack into objects.
SegmentStack() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
SegmentStackIntoObjectsPooled<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.stack: A base class for algorithms to segment a stack into one or more objects - using a pool of models (e.g.
SegmentStackIntoObjectsPooled() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled
SegmentText - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack: Extracts text from a RGB image by using the EAST deep neural network model
SegmentText() - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
SegmentThresholdAboveMinBound - Class in org.anchoranalysis.plugin.mpp.bean.segment.binary
SegmentThresholdAboveMinBound() - Constructor for class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
SegmentWithMarkedPointProcess - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks: Segments a channel with marked pointed processes.
SegmentWithMarkedPointProcess() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
SegmentWithSeeds - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment: Takes each object one-by-one from objectsSource, and finds matching seeds from objectsSeeds
SegmentWithSeeds() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
select(ExperimentExecutionArguments) - Method in class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
select(ExperimentExecutionArguments) - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam: Retrieves the parameter.
select(ExperimentExecutionArguments) - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.All
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.FromStacks: Takes a stack-collection and extracts a set of references to particular channels (each with a name)
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase: Selects a StackWriter to use as a delegate.
SelectDimensions - Enum in org.anchoranalysis.image.voxel.object.morphological
SelectDimensionsFactory - Class in org.anchoranalysis.image.voxel.object.morphological
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.SerializedGenerator
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.tabular.CSVGenerator
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.text.StringGenerator
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.xml.XMLGenerator
SelectFromShared<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list: Selects a number of features of shared-features matching against a regular-expression
SelectFromShared() - Constructor for class org.anchoranalysis.feature.bean.list.SelectFromShared
selectIndexToRmv(MarkCollection, ProposerContext) - Static method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
selective() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters: A writer that allows only certain selected output-names, and records the written output-names
selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.UniformRandom
selectMarkFrom(MarkCollection, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkFromCollectionProposer
selectMarkFrom(MarkCollection, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
selectOutputEnabled(Optional<OutputEnabledRules>) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules: Selects which OutputEnabledRules to employ.
SelectParam<T> - Interface in org.anchoranalysis.launcher.executor.selectparam: Different methods of selecting a object T that is used as a parameter for an experiment.
SelectParamFactory - Class in org.anchoranalysis.launcher.executor.selectparam: Creates an appropriate SelectParam based upon the options passed to the command-line.
SelectSlicesBase - Class in org.anchoranalysis.plugin.mpp.bean.region
SelectSlicesBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
SelectSlicesWithIndexBase - Class in org.anchoranalysis.plugin.mpp.bean.region
SelectSlicesWithIndexBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
separate(Collection<T>) - Method in class org.anchoranalysis.spatial.rtree.SpatiallySeparate: Splits the collection of objects into spatially separate clusters, without consuming all elements in elements.
separateConsume(Set<T>) - Method in class org.anchoranalysis.spatial.rtree.SpatiallySeparate: Splits the collection of objects into spatially separate clusters, consuming all elements in elements.
Sequence - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Performs a sequence of succesive segmentations
Sequence() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
SequencedDirectory - Interface in org.anchoranalysis.io.manifest.directory.sequenced
SequencedDirectoryDeserializer<T> - Class in org.anchoranalysis.io.manifest.directory.sequenced: Applies a deserializer to each file in a directory with a sequence of files.
SequencedDirectoryDeserializer(SequencedDirectory, Deserializer<T>) - Constructor for class org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectoryDeserializer: Creates from a manifest-directory entry.
SequenceInteger - Class in org.anchoranalysis.bean.permute.property: A sequence of integers.
SequenceInteger() - Constructor for class org.anchoranalysis.bean.permute.property.SequenceInteger
SequenceMemory - Class in org.anchoranalysis.io.generator.sequence
SequenceMemory() - Constructor for class org.anchoranalysis.io.generator.sequence.SequenceMemory
SequenceType<T> - Class in org.anchoranalysis.io.manifest.sequencetype: A sequence of elements (of type T), which are mapped to a range of integer indices.
SequenceType() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.SequenceType
SequenceTypeException - Exception in org.anchoranalysis.io.manifest.sequencetype
SequenceTypeException(Exception) - Constructor for exception org.anchoranalysis.io.manifest.sequencetype.SequenceTypeException
SequenceTypeException(String) - Constructor for exception org.anchoranalysis.io.manifest.sequencetype.SequenceTypeException
SequentialProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor: Executes jobs sequentially
SequentialProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.SequentialProcessor
SequentialSession<T extends FeatureInput> - Class in org.anchoranalysis.feature.session: Calculates features with successively different parameters, taking care of caching etc.
SerializedGenerator<T> - Class in org.anchoranalysis.io.generator.serialized
SerializedGenerator(Optional<String>) - Constructor for class org.anchoranalysis.io.generator.serialized.SerializedGenerator
SerializedObjectSupplier<T> - Interface in org.anchoranalysis.io.manifest.finder: Supplies a serialized-object (if it exists)
serializeObjectToFile(T, Path) - Static method in class org.anchoranalysis.core.serialize.XStreamSerializer: Writes a file with a serialized representation of an object.
SessionInput<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache: Encapsulates a feature-input in the context of a particular session.
SessionInputSequential<T extends FeatureInput> - Class in org.anchoranalysis.feature.session: A feature-input that will be used in a SequentialSession
SessionInputSequential(T, CacheCreator) - Constructor for class org.anchoranalysis.feature.session.SessionInputSequential: Constructor
SessionInputSequential(T, CacheCreator, FindChildStrategy) - Constructor for class org.anchoranalysis.feature.session.SessionInputSequential
set() - Method in class org.anchoranalysis.bean.StringSet
set(int, double) - Method in class org.anchoranalysis.feature.results.ResultsVector
set(int, ResultsVector) - Method in class org.anchoranalysis.feature.results.ResultsVector
set(int, Seed) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
set(int, Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
set(int, UpdatableMarkSet) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
setAboveMaxValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Constant to return if outside the range (above the maximum allowed)
setAcceptNoResolution(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
setAcceptOutsideScene(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
setAdd(DefineAdderBean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setAddCriteria(AddCriteria<T>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
setAdditionalBackgrounds(List<DerivePath>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Additional background-stacks that are possible to use while annotating.
setAdditionalChannels(List<ChannelEntry>) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick: Additional channels other than the main one, which are located in the main raster file
setAdditionalChannels(List<ChannelEntry>) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: Additional channels other than the main one, which are located in the main raster file
setAdditionalPropertyPaths(StringSet) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath: Additional property paths that are also changed, along with the main propertyPath *
setAddName(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setAddOne(boolean) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
setAddSum(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum: Added to all gradients (so we can store negative gradients)
setAdjacentChannels(List<AdjacentFile>) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: Channels that are located in a separate raster file adjacent to the main raster file
setAggIntervalLog10(double) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval: How many iterations before printing a new report? Encoded in log10.
setAggregateTriggerBank(AggregateTriggerBank<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
setAll(EnergySavedAll) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component
setAngleDegrees(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
setAngleRadians(double) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
setAnnealScheme(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
setAnnotations(AnnotationInputManager<NamedChannelsInputPart, T>) - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
setAnnotatorStrategy(S) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
setAppendChannels(List<AppendStack>) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: Channels that are located in a separate raster file somewhere else in the project's structure
setAppendCsv(AppendCsv) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
setAppendCSV(DerivePath) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
setAppendHistogram(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
setAppendObjects(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager: Appends object-collections to the multi-input
setAppendStack(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
setApplyResolution(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D: Multiples the values by the x-resolution, if it exists.
setArrange(ArrangeStack) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
setArrange(ArrangeStackBean) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
setAsMemberFlag(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
setAsPercentage(boolean) - Method in class org.anchoranalysis.feature.bean.results.Quantile: If true, the quantile is interpreted as a percentage rather than a decimal
setAssigner(AnnotationComparisonAssigner<T>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
setAssignMode(AssignMode<S, T, U>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
setAvoidBulletOnFirst(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate: Iff true no bullet is added for the very first-item in the list
setAvoidDivideByZero(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
setAvoidOverlappingObjects(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: If true, no overlapping objects are treated as pairs
setAxis(String) - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector: Which axis the unit-vector will align with.
setAxis(String) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
setAxis(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis: Which axis? X=0, Y=1, Z=2
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation: Which axis to read from (x,y,z)
setAxis(String) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
setAxisColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
setAxisMax(double) - Method in class org.anchoranalysis.plot.AxisLimits
setAxisMin(double) - Method in class org.anchoranalysis.plot.AxisLimits
setBackground(AnnotationBackground) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
setBackground(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The background.
setBackgroundChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Uses only this channel (identified by an index in the stack) as the background, -1 disables.
setBackgroundChannelName(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
setBackgroundChannelProvider(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
setBackgroundColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
setBackgroundID(String) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setBackgroundStackMap(StringMap) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-null, maps underlying stack-name to a background
setBackgroundStackName(String) - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
setBeanExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
setBeanExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
setBelowMinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: Constant to return if outside the range (below the minimum allowed)
setBest(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask: If true uses 8 neighborhood rather than 4 neighborhood etc.
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents: if true, uses 8 neighborhood instead of 4, and similarly in 3d
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
setBinaryInputChannelID(String) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform: The ID of the binary input mask that determines the region of the watershed
setBinarySgmn(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
setBirthRepeats(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
setBit0(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
setBit1(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
setBit2(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
setBit3(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
setBit4(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
setBit5(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
setBit6(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
setBit7(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
setBitsPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
setBlockSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The block-size as per OpenCV implementation (identical default-size)
setBlockStride(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The block-stride as per OpenCV implementation (identical default-size)
setBlue(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
setBlue(int) - Method in class org.anchoranalysis.core.color.RGBColor
setBlue(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
setBorderWidth(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Adds a border around each part of the montage
setBoundCalculator(BoundCalculator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
setBoundCalculator(BoundCalculator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
setBounds(RotationBounds) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
setBoundsRatio(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
setBoundType(BoundChangeEvent.BoundType) - Method in class org.anchoranalysis.core.index.bounded.BoundChangeEvent
setBridgeMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each input-object to an intermediary-object
setBundleSize(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
setBundleSize(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
setBySlices(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
setCacheSize(int) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches: Size of feature evaluation cache for featureEvaluatorMatch
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: Method to calculate the level for a particular object.
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold: Calculates the level for the threshold
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
setCalculateLevelElse(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
setCellDefault(ArrangeStackBean) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
setCells(List<Cell>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
setCellSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The cell-size as per OpenCV implementation (identical default-size)
setCenterPoint(Point3d) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
setChangeExisting(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase: If true, the existing channel can be changed.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A channel that is provided to the stack.
setChannel1(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
setChannel1(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
setChannel2(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
setChannel2(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
setChannel3(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
setChannelAssignFrom(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
setChannelConversionStyle(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: To convert as RGB or independently or in another way
setChannelConverter(ConvertChannelTo) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
setChannelConverter(ConvertChannelTo) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: Optionally, how to convert from one bit-depth to another (scaling, clipping etc.)
setChannelElse(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
setChannelFilter(ChannelFilter) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: Optionally, includes only certain channels when converting.
setChannelFirst(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of first channel
setChannelGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
setChannelID(String) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: The ID of the channel that provides the input to the filter
setChannelIfVoxelZero(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero: If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick: If either stackAsChannel==true or we have specified additionalChannels this indicated which channel to use from the stack
setChannelLookup(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
setChannelMap(ChannelMap) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
setChannelMask(String) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: If defined, this is the name of channel used as a mask over the values which are fed into the histogram
setChannelName(String) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
setChannelName(String) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack: By default all channels are converted into a stack.
setChannelNum(Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
setChannelSecond(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Index of second channel
setChannelsExtra(List<ChannelProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setChannelsPerByteArray(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
setChannelThreshold(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
setCheck(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
setCheckMark(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
setCheckMark(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
setCheckMark(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
setCheckParsedFilePathBag(CheckParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles: Imposes a condition on each parsedFilePathBag which must be-fulfilled if a file is to be included
setClassifierProvider(FeatureListProvider<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
setClearOutsideMask(boolean) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
setCol(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
setCollapseFilename(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
setCollectionID(String) - Method in class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
setCollectionID(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
setColor(RGBColorBean) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle: The single color to repeat.
setColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: An optional color associated with the label when displayed via GUI
setColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
setColors(List<RGBColorBean>) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList: The list of colors to specify
setColors(ColorScheme) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary: The delegate that creates the (unshuffled) list.
setColors(ColorScheme) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator: Colors to use for drawing objects
setColorScheme(ColorScheme) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
setColorsUnpaired(ColorScheme) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
setColorUnselectedObjects(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Optionally outline the other (unselected for the thumbnail) objects in this particular color.
setColumnDefinition(ColumnDefinition) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV: Column definition for the CSVfiles
setColumnFirstNumberPixels(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with the number of pixels for the first Object
setColumnFirstPointX(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with X coordinate of point for the first Object
setColumnFirstPointY(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with Y coordinate of point for the first Object
setColumnFirstPointZ(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with Z coordinate of point for the first Object
setColumnGroup(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition: Name of CSV column used to group results (the same values, are outputted together)
setColumnID(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition: Name of CSV column with the file identifier
setColumnNumPixels(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single: Name of CSV column with the number of pixels for the first Object
setColumnPointX(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single: Name of CSV column with X coordinate of point for the first Object
setColumnPointY(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single: Name of CSV column with Y coordinate of point for the first Object
setColumnPointZ(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single: Name of CSV column with Z coordinate of point for the first Object
setColumns(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: How many columns to use in the montage, or 0 to guess an approximately square output
setColumnSecondNumberPixels(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with the number of pixels for the second Object
setColumnSecondPointX(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with X coordinate of point for the first Object
setColumnSecondPointY(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with Y coordinate of point for the first Object
setColumnSecondPointZ(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise: Name of CSV column with Z coordinate of point for the first Object
setCombine(CombineObjectsForFeatures<T>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
setCommand(String) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation: One of: open, close, fill, erode, dilate, skel, outline
setComparerLeft(Comparer) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
setComparerRight(Comparer) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
setCondition(KeyValueCondition) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
setCondition(KeyValueCondition) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
setConfidenceThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects: The maximum difference in confidence for merging.
setConstant(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
setConstantBound(ResolvedBound) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
setContains(String) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
setContains(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must contain (case-sensitive) this string.
setConvert(ConvertChannelToWithHistogram) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
setConvexHull(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects: If true, Reduces the set of points by applying a convex-hull operation
setCopyFilesMethod(CopyFilesMethod) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
setCopyFilesNaming(CopyFilesNaming) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
setCopyFilesNaming(CopyFilesNaming) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
setCountThreshold(int) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: If there are more than countThreshold elements, use summarizerGreaterThan, else summarizerElse.
setCov(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
setCreateMark(CreateMarkFromPoints) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
setCreateShort(boolean) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew: If True creates an unsigned short-image
setCsvFilePath(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
setCsvIgnoreZeros(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: Iff true, bins with zero-counts are not written as a row in the CSV file.
setCurrentTemp(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
setCustomName(String) - Method in class org.anchoranalysis.feature.bean.Feature: An optional additional name that be associated with the feature (defaults to an empty string)
setDatasetName(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: The name of the experiment including version suffix
setDatasetNameSubdirectory(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: If true the datasetName is appended as a subdirectory e.g.
setDatasets(StringSet) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
setDatasets(StringSet) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
setDatasetSpecific(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
setDatasetSpecific(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
setDatasetSuffix(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase: A suffix appended to the dataset name extracted from the reg exp
setDatasetVersion(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: A version-suffix appended to the dataset name extracted from the reg exp
setDay(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If true, the current day (yyyy.MM.dd) is included in the output
setDebug(boolean) - Method in class org.anchoranalysis.bean.shared.path.RootPath: If true this root is preferred, when executing a job in debugging mode
setDebug(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
setDefaultBehaviourString(Optional<String>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: If present, a string is printed in the description if the default-experiment is used, otherwise ignored.
setDefaultColors(ColorScheme) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: The default color-scheme used for outputs, if no other scheme is specified.
setDefine(Define) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
setDefine(Define) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
setDefine(DefineOutputterMPP) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop: Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
setDefine(DefineOutputterMPP) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
setDefine(DefineOutputterMPP) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
setDefine(DefineOutputterMPPWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
setDefine(DefineOutputterMPPWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Adds definitions of stacks/objects etc.
setDelaySizeAtEnd(int) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
setDelegate(ResolvedBound) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
setDelimiter(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
setDelta(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setDeltat(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
setDestinationFolderPath(FilePath) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Dimensions to create new mask
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
setDimensionsSource(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
setDimensionsTarget(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
setDirection(DirectionVectorBean) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance: Direction of the distance being converted, defaults to a unit vector along the X-axis
setDirection(VectorInDirection) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
setDirectionVector(VectorInDirection) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
setDirectory(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory: A relative-path (to the user home directory) which is used as an output directory
setDirectory(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
setDirectoryDistance(int) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment: How many directories to recurse back from the current file to the Experiments/ directory
setDisableDebugMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
setDisableDebugMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
setDisablePathModification(boolean) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
setDistance(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors: How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
setDistance(MarkDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
setDistanceMapProvider(ChannelProvider) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters: A distance map which can also be used for making decisions on merging
setDistanceMax(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
setDistanceTransformMultiplyBy(double) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform: Multiplies the distance transform by this factor to make it more meaningful in a short
setDistanceTransformSmoothSigmaMeters(double) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform: If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below
setDistanceX(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
setDistanceY(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
setDistanceZ(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
setDistanceZEndIfEmpty(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
setDivideByZeroValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
setDivisor(double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble: Divide by
setDivisor(int) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo: What the identifier is divided by to find the modulo.
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Whether to perform the morphological dimensions in 3D or 2D
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
setDummyMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
setDuplicate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference: If true the channel is duplicated after it is retrieved, to prevent overwriting existing data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
setDuplicate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference: If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
setElemAllCreator(FeatureListProvider<FeatureInputAllMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
setElement(T) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
setElemIndCreator(FeatureListProvider<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
setElemPairCreator(FeatureListProvider<FeatureInputPairMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
setEmptyValue(double) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
setEmptyValue(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
setEnd(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: An index beyond which we cannot iterate (inclusive)
setEnd(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
setEnergyChannelIndexCheck(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
setEnergyChannelIndexFail(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels: Index of which channel in the energy-stack to select
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase: Index of which channel in the energy-stack to select
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel: Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: The channel that that forms the histogram
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask: The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
setEnergyIndexGradient(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
setEnergyIndexMask(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: A channel of the energyStack that is used as an additional mask using default byte values for ON and OFF
setEnergyIndexMask(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Optionally, index of another channel that masks the histogram.
setEnergyIndexX(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
setEnergyIndexY(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
setEnergyIndexZ(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
setEnergyParamsName(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop: If non-empty, A keyValueParams is treated as part of the energyStack
setEnergySchemeCreator(EnergySchemeCreator) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
setEnergySchemeCreator(EnergySchemeCreator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Creates an energy scheme that assigns an energy score to each collection of marks.
setEnergyStack(Optional<EnergyStack>) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
setEnergyStack(EnergyStack) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
setEnergyTotal(double) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The pre-annealed total energy
setEnergyTotal(double) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
setEquals(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must be exactly equal to (case-sensitive) this string.
setErodeAtBoundary(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
setError(int, Exception) - Method in class org.anchoranalysis.feature.results.ResultsVector
setErrorAll(Exception) - Method in class org.anchoranalysis.feature.results.ResultsVector
setErrorDisconnectedObjects(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels: If true, throws an error if there is a disconnected object after the erosion
setErrorTree(DefaultTreeModel) - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
setExactDepth(int) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
setExceptionIfEmpty(boolean) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic: If true, then an exception is thrown if the histogram is empty, otherwise is returned.
setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Iff true, zero-valued voxels are excluded from the histogram
setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity: If true, zeros are excluded from considering in the histogram
setExecutionTime(long) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
setExitBeforeOptimization(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Iff true the algorithm exits before optimization begins (useful for debugging).
setExitWithMinima(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong: If true, exits early and just returns the minima, without any further segmentation
setExperimentIdentifier(ExperimentIdentifier) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: A name for the experiment.
setExperimentIdentifier(ExperimentIdentifier) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase: A folder identifying the type of experiment (where the outputs are all put in the same directory
setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: A folder identifying the type of experiment (where the outputs are all put in the same directory
setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment: The value of $1 (see comment above) in naming-structure.
setExpression(String) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
setExtendInZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages: Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all slices)
setExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
setExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
setExtra(double) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
setExtractScoreSize(ExtractScoreSize<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
setExtractScoreSize(ExtractScoreSize<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
setExtractScoreSizeReport(ExtractScoreSize<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
setExtractScoreSizeState(ExtractScoreSize<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
setExtractWeight(ExtractWeightFromMark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
setFactor(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
setFactor(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
setFactorHigh(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
setFactorLow(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
setFactorStdDev(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
setFallback(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
setFallbackName(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If there's no task-name, then this constant is used as a fallback name
setFeature(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects: Feature that calculates the score for an object.
setFeature(Feature<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
setFeature(Feature<T>) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
setFeature(Feature<T>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session
setFeature(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
setFeature(FeatureListElem<T>) - Method in class org.anchoranalysis.feature.bean.list.ListSequence: The list feature that is duplicated, and populated.
setFeature(FeatureProvider<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
setFeature(FeatureProvider<T>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
setFeatureCondition(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
setFeatureCondition(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange: Calculates value for the condition - which is checked if it lies within a certain range
setFeatureElse(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
setFeatureEvaluator(FeatureEvaluator<T>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
setFeatureEvaluatorMatch(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
setFeatureEvaluatorMerge(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
setFeatureEvaluatorThreshold(FeatureEvaluator<FeatureInputNull>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Allows merge only if the feature-value satisfies a relation to this threshold
setFeatureListRef(String) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
setFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: Features to calculate for objects in the features output.
setFeatures(List<NamedBean<FeatureListProvider>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: The features to be exported (after possibly some manipulation or augmentation)
setFeatures(List<FeatureProvider<T>>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator: A list of providers, combined together to form a list of features, to be calculated in a session
setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Features applied to each group to aggregate values (takes FeatureResultsVectorCollection)
setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Additional features that only depend on the image, so do not need to be replicated for every object.
setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Additional features that are processed on the pair of images (i.e.
setFeatureTables(List<OutputFeatureTable>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop: Specifies a feature-table that can also be outputted.
setFeedbackReceiver(FeedbackReceiverBean<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Processes feedback from the segmentation algorithm for outputting / debugging.
setFeedbackReceiver(FeedbackReceiverBean<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
setFileFilter(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: Files to search for
setFileId(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv: Unique identifier for the stack, object-mask-collection etc.
setFileId(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManagerWithFileID: Unique identifier for the stack, object-mask-collection etc.
setFileInput(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment: A string indicating the input file(s)
setFileInput(InputManager<FileInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
setFileInput(InputManager<FileInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
setFileInput(NamedFiles) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
setFileName(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
setFilenamePrefix(String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
setFilePath(String) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
setFilePath(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
setFilePath(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
setFilePath(Path) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
setFilePathParser(FilePathParser) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
setFilePathParser(FilePathParser) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
setFilePathPrefixer(PathPrefixer) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Determines a prefix to use when outputting a file based upon an input-path.
setFilePathPrefixer(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
setFilePathPrefixer(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
setFilePathProviderSVM(FilePathProvider) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
setFilePrefix(String) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
setFilesProvider(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
setFilesProvider(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles: The files to use as inputs.
setFilesProvider(FilesProviderWithDirectory) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
setFilesProvider(FilesProviderWithDirectory) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: A path to the main channel of each file
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
setFilter(ImageLabeller<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
setFilterFilesCsv(MatchedAppendCsv) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: If set, a CSV is read with two columns: the names of images and a
setFindMaxima(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice: If true, the maxima of the score is searched for.
setFindOutlinePixelAngle(FindPointOnOutline) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
setFirst(boolean) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle: Iff true, first object is used, otherwise the second
setFirst(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the first-level.
setFirst(StateTransformerBean<S, U>) - Method in class org.anchoranalysis.mpp.segment.transformer.Compose: First transformation from S to U
setFirstLineHeaders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setFixRandomSeed(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Iff true uses a constant seed for the random-number-generator (useful for debugging).
setFlatten(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline: If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D
setFlatten(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced
setFolderDataset(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
setFolderOutput(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
setForceBinary(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
setForceChangeBytes(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.
setForceDetailedLogging(boolean) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Whether more detailed log-messages around each experiment occur.
setForceEagerEvaluation(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setForceReader(String) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader: If non-empty forces usage of a particular bioformats plugin
setForceRGB(boolean) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster: If set, ensures every stack is converted into 3 channels
setForwardDirectionOnly(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
setFrom3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject: A sorted-set of three-dimensional integer points from the entire object-mask
setFromOutline(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
setGaussian(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: If true, the Gaussian filter is included
setGaussianSigmaMeters(double) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
setGradient(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setGraphColorScheme(PlotColorScheme) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
setGrayscaleReconstruction(GrayscaleReconstructionByErosion) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
setGreen(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
setGreen(int) - Method in class org.anchoranalysis.core.color.RGBColor
setGreen(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
setGroup(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Specifies a group for the label (similar labels that are displayed together)
setGroup(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
setGroup(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
setGroup(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: If non-null this file-path is used to determine the group of the file If null, no group is included.
setGroup(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: If defined, translates a file-path into a group.
setGroupNum(int) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
setHeight(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
setHighestTwoRadiiOnly(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram: If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional histogram of voxel intensity values which can be used by segment
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram: The histogram to plot.
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram: If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
setHistogramChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
setHistogramIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
setHistogramsExtra(List<HistogramProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setHistogramsOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.

What's allowed or not when outputting histograms
setHorizontalAlign(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
setId(int) - Method in class org.anchoranalysis.mpp.mark.Mark
setId(int) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
setId(String) - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
setId(String) - Method in class org.anchoranalysis.feature.bean.operator.Reference
setId(String) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
setId(String) - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
setId(String) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
setId(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects: ID for the particular object-collection
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
setId(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
setId(String) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
setId(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Translates an input file name to a unique ID
setIdentifierSuffix(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
setIdentifierSuffix(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
setIdGenerator(DerivePath) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
setIdGetter(IdentifierGetter<T>) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
setIgnoreAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
setIgnoreCase(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
setIgnoreContains(String) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-empty any stackNames (after map) containing a certain string will be ignored
setIgnoreFileNotFoundAppend(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setIgnoreFittingFailure(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects: If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply not included (with only a log error) If false, an exception is thrown
setIgnoreHidden(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
setIgnoreHigherSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
setIgnoreLowerSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
setIgnoreMissingChannel(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels: Iff true and we cannot find a channel in the file, we ignore it and carry on
setIgnoreNaN(boolean) - Method in class org.anchoranalysis.feature.bean.operator.Sum: If true, we ignore any NaN values.
setIgnoreNoObjects(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: If true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.
setIgnoreRangeAxisOutside(boolean) - Method in class org.anchoranalysis.plot.index.LinePlot
setIgnoreZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
setImageLabeller(ImageLabeller<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: Maps a label to an image
setImgChannelMapCreator(ChannelMap) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
setIncludeFeatureNames(boolean) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features
setIncludeFileName(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
setIncludeFirst(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the First-object of the pair
setIncludeFolders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure: If false, the folders are ignored, and only the file-name is used in the output
setIncludeMerged(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Merged-object of the pair
setIncludeSecond(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors: Include features for the Second-object of the pair
setIncludeShell(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
setIncludeZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
setIncrement(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: Size of step to use when incrementing
setIncrementDegrees(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
setIncrementDegrees(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
setIndex(int) - Method in interface org.anchoranalysis.core.index.IndexSetter
setIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
setIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt: Index in z-dimension of slice to extract
setIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase: Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
setIndex(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
setIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
setIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
setIndex(int) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: Which index to return from the HOG descriptor
setIndex(int, double) - Method in class org.anchoranalysis.image.core.orientation.DirectionVector: Sets an element of the vector by the index of its position, index=0 is the X-element, index=1 is the Y-element etc.
setIndexNonZero(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
setInitContext(OptimizationContext) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
setInitialKernel(Kernel<T>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
setInnerCoreDistance(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
setInPathPrefix(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
setInput(InputManager<? extends ProvidesStackInput>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
setInput(InputManager<NamedChannelsInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
setInput(InputManager<NamedChannelsInputPart>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setInput(InputManager<T>) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
setInput(InputManager<T>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: The input-manager to specify where/which/how necessary inputs for the experiment occur.
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.Shuffle
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
setInput(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
setInput(MultiInputManager) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
setInputDebug(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
setInputDirectory(Optional<Path>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
setInputFilterExtensions(Optional<Set<String>>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments: If defined, a set of extension filters that can be applied on inputDirectory
setInputFilterGlob(Optional<String>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments: If non-null, a glob that is applied on inputDirectory
setInputName(String) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
setInputName(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
setInputName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
setInputPaths(List<Path>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
setInputPointShift(float) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
setIntensity(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setInterpolate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
setInterpolator(InterpolatorBean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
setInterpolator(InterpolatorBean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Interpolator used when scaling the background
setInterpolator(InterpolatorBean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
setInverse(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
setInverse(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is removed)
setInverseMask(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
setInvert(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
setInvert(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
setInvert(boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch: Iff true, then a file is rejected if regEx matches and vice-versa (opposite to normal behaviour)
setInvertDecisionValue(boolean) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity: Feature to apply to the histogram
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity: Feature to apply to the histogram
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity: Feature to apply to the histogram
setItem(Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
setItem(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
setItem(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
setItem(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoOne
setItem(Feature<S>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
setItem(Feature<T>) - Method in class org.anchoranalysis.feature.bean.list.DefineSingle
setItem(FeatureListProvider<FeatureInput>) - Method in class org.anchoranalysis.feature.bean.list.PrependName
setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: For each feature in the list, a corresponding "aggregate" feature is created in the output list
setItem(FeaturePairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
setItem(VoxelScore) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
setItem(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
setItem(ReportFeature<MPPInitParams>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
setItem(T) - Method in class org.anchoranalysis.bean.NamedBean: The item that is to be named (i.e.
setItem(T, int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
setItem1(Feature<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
setItem2(Feature<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
setItemMean(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
setItemProportionate(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
setItemStdDev(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
setIterations(int) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat: The maximum number of iterations.
setIterations(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
setIterations(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
setIterations(int) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation: iterations for erode, dilate, open, close
setIterations(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection: The number of dilations and erosions to apply to determine if two objects intersect
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase: The number of dilations and erosions to apply and whether to do in the Z dimension
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell: The number of dilations and erosions to apply and whether to do in the Z dimension
setIterationsDilation(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological dilation
setIterationsErosion(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: Number of times to perform morphological erosion
setJobNumber(int) - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
setJobShortName(String) - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
setKappa(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
setKeepEntireImage(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages: If true, rather than writing out a bounding-box around the object-mask, the entire image is written
setKeepExtremes(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
setKeepProcessorsFree(int) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor: How many processors to avoid using for the tasks.
setKeepProcessorsFree(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: How many processors to avoid using for the tasks.
setKeepZ(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Keep the z-resolution if it is already defined
setKernel(Kernel<T>) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
setKernel(Kernel<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
setKernelFactoryList(WeightedKernelList<?>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
setKernelHalfWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median: Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
setKernelNegative(KernelPosNeg<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
setKernelPositive(KernelPosNeg<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
setKernelProposer(KernelProposer<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Proposes kernel-changes during iterations of hte marked-point-processes.
setKernelStateBridge(KernelStateBridge<U, T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
setKey(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
setKey(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
setKeyGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
setKeyLower(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
setKeyMean(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
setKeyPrefix(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param: Prefix prepended to key
setKeyRequired(boolean) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
setKeyStdDev(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
setKeySuffix(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
setKeyUpper(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
setKeyValueParamsID(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
setKeyValueParamsID(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage: If non-empty, the identifier of a key-value-params collection that is passed to the segmentation procedure.
setLabel(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: If true a label is added beside every image showing the slice index
setLabels(List<AnnotationLabel>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
setLevel(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
setLine(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
setList(List<DefineAdderBean>) - Method in class org.anchoranalysis.bean.define.adder.Concatenate
setList(List<NamedBean<FeatureListProvider<T>>>) - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed
setList(List<NamedBean<FromStack>>) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
setList(List<Provider<Stack>>) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
setList(List<RegEx>) - Method in class org.anchoranalysis.bean.shared.regex.RegExList
setList(List<StringMapItem>) - Method in class org.anchoranalysis.bean.shared.StringMap
setList(List<LoggingDestination>) - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple: The list of loggers to log to
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.Define
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
setList(List<ObjectFilter>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine: A list of other filters from which the sub-classes implement filtering behaviour.
setList(List<ColorProvider>) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
setList(List<ObjectCollectionProvider>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
setList(List<BinarySegmentation>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence: A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
setList(List<CalculateLevel>) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
setList(List<ProviderAsStack>) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
setList(List<ChannelEntry>) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
setList(List<FilesProvider>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Combine
setList(List<InputManager<T>>) - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate
setList(List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
setList(List<RegionMembership>) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
setList(List<AddCriteriaPair>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
setList(List<CheckMark>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
setList(List<TerminationCondition>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
setList(List<FeedbackReceiver<T>>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
setList(List<Summarizer<T>>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
setList(List<VisitScheduler>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
setList(List<VisitScheduler>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
setList(FeatureList<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
setListAdditionalChannelProviders(List<ChannelProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
setListAppend(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setListAppend(List<FilePathBaseAppendToManager>) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick: Additional entities that are appended to the multi-input
setListAppendFilePath(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
setListAppendKeyValueParams(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
setListAppendMarks(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
setListAppendMarksFromAnnotation(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
setListAppendMarksFromAnnotationAcceptedOnly(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
setListAppendMarksFromAnnotationRejectedOnly(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
setListComparers(List<NamedBean<Comparer>>) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
setListFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
setListImageFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
setListReportFeatures(List<ReportFeature<DeserializedManifest>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
setListReportFeatures(List<ReportFeatureForSharedObjects>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
setListStackProvider(List<NamedBean<StackProvider>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages: The channels we extract the object-masks from - all assumed to be of same dimension
setListStackProviderMIP(List<NamedBean<StackProvider>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages: The channels we extract the object-masks from - all assumed to be of same dimension
setLog(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf: The logger to use if conditions are fulfilled
setLog(LoggingDestination) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
setLogExperiment(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: Where log messages that do not pertain to a specific job (input) appear.
setLogExperimentPath(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment: Relative path to a logger for the experiment in gneeral
setLoggerTaskCreator(LoggingDestination) - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
setLogPath(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the pathIn and pathOut are logged.
setLogTask(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: Where log messages that do pertain to a specific job (input) appear.
setLogTaskPath(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment: Relative path to a logger for a specific task
setLookup(StringList) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
setMainChannelIndex(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: Index of the mainChannel
setMainChannelName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: The name of the channel provided by the rasters in file Provider
setManifestDescriptionFunction(String) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
setManifestDeserializer(ManifestDeserializer) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
setManifestExperimentInputFileSet(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
setManifestFunction(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
setManifestFunction(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
setManifestInputFileSet(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
setMap(StringMap) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
setMarkBounds(MarkBounds) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
setMarkBounds(MarkBounds) - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
setMarkEvaluator(NamedBean<MarkEvaluator>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: A mark-evaluator that is added to the GUI to support this annotation
setMarkFactory(MarkFactory) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
setMarkFactory(MarkWithIdentifierFactory) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
setMarkFactory(MarkWithIdentifierFactory) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: Creates a new mark, before perhaps further manipulations by a kernel.
setMarkFromMarksProposer(MarkFromCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
setMarkProposer(String) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Name of the MarkProposer to use.
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
setMarkProposerAdditionalBirth(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
setMarkProvider(Provider<Optional>) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
setMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The marks
setMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
setMarks(Point2d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setMarksColored(ColoredMarks) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
setMarksExplicit(Point3d, Orientation, Point2d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
setMarksOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.

What's allowed or not when outputting configurations
setMarksProposer(MarkCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
setMarksProposer(MarkCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
setMarksProposer(MarkCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
setMask(Provider<Mask>) - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: A mask that is provided to the stack.
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: An optional mask which restricts the algorithm to only parts of the channel where the mask has an ON voxel
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
setMaskElse(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase: Returned instead of mask if the predicate is not satisfied
setMaskFilled(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
setMaskFilled(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
setMaskIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
setMaskOutline(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
setMaskValue(int) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: What voxel value to read as "On" in the mask above.
setMaskValue(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
setMatch(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
setMatch(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
setMatch(RegEx) - Method in class org.anchoranalysis.feature.bean.list.SelectFromShared
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
setMatchString(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
setMax(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
setMax(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
setMax(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
setMax(double) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
setMax(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
setMax(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars: Boundary value indicating maximally-allowed range value
setMax(int) - Method in interface org.anchoranalysis.core.progress.ProgressReporter
setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
setMax(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
setMax(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
setMax(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
setMax(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature: Calculates maximally-allowed range boundary
setMax(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Maximum-boundary for acceptable range
setMaxCost(double) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
setMaxCost(double) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
setMaxDirectoryDepth(int) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint: An optional maximum distance
setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
setMaxDistanceBetweenMinima(UnitValueDistance) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
setMaxDistanceCOG(UnitValueDistance) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters: The maximum distance allowed between center-of-gravities of objects
setMaxDistanceDeltaContour(double) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform: The maximum distance allowed between two seeds in terms of their values in the distance map
setMaxDistanceDeltaContour(double) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters: The maximum distance allowed between the 'distance from contour' values provided from the distanceMap for each point.
setMaxDistanceProposer(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
setMaxDistanceZ(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
setMaxNumber(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
setMaxNumberItems(int) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Limit
setMaxNumberProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor: An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
setMaxNumberProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: Theoretical maximum number of (CPU) processors to use in parallel.
setMaxNumberProcessors(int) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment: An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
setMaxNumberProcessors(int) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
setMaxNumItems(int) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
setMaxNumItems(int) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
setMaxSize(long) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMaxSplitGroups(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
setMaxValue(long) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
setMaxVar(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMaxVolume(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
setMaxX(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Maximum X coordinate inclusive
setMaxY(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Maximum Y coordinate inclusive
setMaxZ(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Maximum Z coordinate inclusive
setMean(double) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic: Mean
setMedian(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters: If true, the median filter is included
setMedianRadiusMeters(double) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
setMerge(boolean) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
setMergedPosTolerance(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
setMergeMarkProposer(MarkMergeProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
setMessage(String) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
setMethod(String) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
setMethod(String) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ: One of the following strings to identify ImageJ's thresholding algorithms (or an empty string for the default).
setMin(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
setMin(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
setMin(double) - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
setMin(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars: Boundary value indicating minimally-allowed range value
setMin(int) - Method in interface org.anchoranalysis.core.progress.ProgressReporter
setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
setMin(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
setMin(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
setMin(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature: Calculates minimally-allowed range boundary
setMin(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Minimum-boundary for acceptable range
setMinConfidence(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum confidence of an element for its object-mask to be included.
setMinConfidence(double) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText: Proposed bounding boxes below this confidence interval are removed
setMinDiff(double) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
setMinDifference(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: A minimum difference, below which 0.0 is returned
setMinDifference(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
setMinDiversity(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMinimaImposition(MinimaImposition) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
setMinimumBoundingBoxVolume(int) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel: Only objects whose bounding-box volume is greater or equal to this threshold are included.
setMinIntensity(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
setMinIntensity(int) - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D: Intensity for thresholding
setMinIntensityValue(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
setMinMaxIgnoreBeforeIndex(int) - Method in class org.anchoranalysis.plot.index.LinePlot
setMinMaxValues(int, int) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
setMinNumberObjects(int) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
setMinNumberPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints: If a contour has less than this number of points, we don't split it, and return it as-is
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares: Only includes squares that have at lesat this number of voxels
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: The minimum number of voxels that must exist in a connected-component to be included.
setMinNumPoints(int) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
setMinNumPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark: If an object has fewer points than before being fitted, we ignore
setMinNumSlices(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
setMinNumZSlices(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
setMinOverlap(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
setMinRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
setMinRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
setMinRadScaleEnd(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
setMinRadScaleStart(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
setMinRatio(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
setMinRatioPointsInsideRegion(double) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
setMinSize(long) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
setMinVal(double) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
setMinVolume(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
setMinVolume(UnitValueVolume) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
setMinVolumeConnectedComponent(UnitValueVolume) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
setMinX(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Minimum X coordinate inclusive
setMinXYRes(double) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
setMinY(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Minimum Y coordinate inclusive
setMinZ(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn: Minimum Z coordinate inclusive
setMip(boolean) - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
setMip(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
setMip(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
setModelDirectory(Path) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
setMultipleComparer(MultipleComparer) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
setMultiplyBy(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
setName(String) - Method in class org.anchoranalysis.bean.define.adder.FromXmlList: The name of the file in the current working directory WITHOUT THE .xml EXTENSION
setName(String) - Method in class org.anchoranalysis.bean.NamedBean: The name associated with item
setName(String) - Method in class org.anchoranalysis.bean.shared.path.RootPath
setName(String) - Method in interface org.anchoranalysis.core.identifier.name.NameValue: Sets the associated namme
setName(String) - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
setName(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
setName(String) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
setName(String) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
setName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile: A name to describe the adjacent file
setName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase: The name of the appended entity
setName(S, String) - Method in interface org.anchoranalysis.bean.permute.ApplyPermutations.NameSetter
setNameLeft(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: Assigns each input a unique compact name.
setNameRight(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
setNavigateHigherDirs(int) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: Search x number directories higher than file
setNewNameOnFeature(Feature<? extends FeatureInput>, String, String) - Static method in class org.anchoranalysis.feature.bean.list.PrependName
setNoBlack(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
setNormalize(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
setNormalize(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
setNormalizeFeatures(boolean) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier: Normalize features
setNumberChannels(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
setNumberColors(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
setNumberDilations(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
setNumberFrames(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
setNumberGPUProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: How many GPU processors to use when this is possible as a substitute for a CPU processor
setNumberLoopPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
setNumberPoints(int) - Method in class org.anchoranalysis.plot.index.LinePlot
setNumberSubdirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories: How many directories to include in the name.
setNumBins(int) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The number of bins in each histogram for a cell
setNumCols(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
setNumDecimalPlaces(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
setNumLeadingZeros(int) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
setNumLevelsGrouping(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
setNumMarks(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
setNumRep(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
setNumRep(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
setNumRows(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
setObjectMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge: Used to match each intermediary-object to a final-object
setObjects(List<NamedBean<ObjectCollectionProvider>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
setObjects(Provider<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: The objects for whom a level is calculated
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects: Objects to draw on a background
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
setObjects(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.

What's allowed or not when outputting object-collections
setObjects(OutputEnabled) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
setObjects1(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: First collection with items to be merged
setObjects2(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise: Second collection with items to be merged
setObjectsBlue(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
setObjectsContainer(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
setObjectsElse(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
setObjectsGreater(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
setObjectsGreen(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
setObjectsGrouped(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
setObjectsLesser(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
setObjectsRed(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
setObjectsRejected(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
setObjectsSave(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Saves all objects that are inputs to the merge, outputs from the merge, or intermediate merges along the way
setObjectsSeeds(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
setObjectsSeeds(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
setObjectsSource(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
setObjectsSource(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
setObjectsSplitBy(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
setObjectsTarget(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
setOfConnectedComponentIDs() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
setOff(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
setOff(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
setOn(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
setOn(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
SetOperationFailedException - Exception in org.anchoranalysis.core.index
SetOperationFailedException(String) - Constructor for exception org.anchoranalysis.core.index.SetOperationFailedException
SetOperationFailedException(Throwable) - Constructor for exception org.anchoranalysis.core.index.SetOperationFailedException
setOptimization(OptimizationScheme<VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess: The optimization-scheme that determines which configurations are accepted/rejected from one iteration to the next.
setOptionList(List<KernelProposerOption<T>>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
setOptions(ReadOptions) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
setOptions(ReadOptions) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
setOrientationProposer(OrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
setOrientationXYProposer(OrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
setOutline(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: If true, an outline is drawn around the entries.
setOutlineAtBoundary(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
setOutlineColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The color of the outline
setOutlinePixelsRetriever(OutlinePixelsRetriever) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
setOutlinePixelsRetrieverReverse(OutlinePixelsRetriever) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
setOutlineProvider(MaskProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: The width of the outline (only relevant if outline==true
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: The width of the outline.
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The width of the outline
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
setOutPath(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: Constructs a path as an output, replacing $1, $2 etc.
setOutPathPrefix(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve: A directory in which to output the experiment-directory and files
setOutput(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
setOutput(OutputManager) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment: The output-manager that specifies how/where/which elements occur duing outputting.
setOutput(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
setOutputCSV(boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize: Iff true, a mapping.csv file is created showing the mapping between the original-names and the anonymized versions
setOutputDirectory(Optional<Path>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments: A directory indicating where inputs can be located
setOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.

What's allowed or not - highest level outputs
setOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
setOutputName(String) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileBase: The name to use (without extension) for the text-file log
setOutputName(String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
setOutputName(String) - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle: An identifier used in rules to determine if an output is enabled or not.
setOutputName(String) - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
setOutputName(String) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
setOutputName(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
setOutputName(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
setOutputNameStyle(IndexableOutputNameStyle) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
setOutputRGBOutline(StringSet) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
setOutputRGBOutlineFlattened(StringSet) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
setOutputsDisabled(StringSet) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled: The names of the outputs that are disbled.
setOutputsEnabled(StringSet) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled: The names of the outputs that are enabled.
setOutputsEnabled(OutputEnabledRules) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Which outputs are enabled or not enabled.
setOutputShort(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase: Iff true, outputs a short channel, otherwise byte channel
setOutputStackProvider(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
setOutputWriteSettings(OutputWriteSettings) - Method in class org.anchoranalysis.io.output.bean.OutputManager: General settings (default file extensions, colors etc.) for outtping files.
setOutputWriteSettings(OutputWriteSettings) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
setOutside(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies otside the range
setOutsideAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
setOutsideAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
setOutsideAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
setOverlapRatioThreshold(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
setOverlapThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects: The maximum size for merging.
setPadding(Padding) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase: Padding placed on each side of the outputted image (if it's within the image)
setPaddingXY(int) - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in XY directions
setPaddingZ(int) - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in Z direction
setPairAddCriteria(AddCriteriaPair) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
setPairCollection(RandomCollection<IdentifiablePair>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
setPairTypeClass(Class<?>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
setParam(P) - Method in class org.anchoranalysis.bean.initializable.property.PropertyInitializer: Sets the current parameters used for propagation
setParamMean(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
setParamPrefix(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
setParamPrefixAppendNumber(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder: If true the constant is appended to the param prefix (a dot and a number)
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
setParams(KeyValueParams) - Method in class org.anchoranalysis.feature.energy.EnergyStack
setParams(HOGParameters) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor: Parameters used for calculating HOG
setParams(HOGParameters) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: Parameters used for calculating HOG
setParamStdDev(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
setPath(String) - Method in class org.anchoranalysis.bean.shared.path.RootPath: A path on a filesystem to the directory, that defines the root
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
setPathAnnotation(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
setPathDefaultMarks(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
setPathLabel(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller: Path to a CSV label file (comma-separated, with header, no quotes)
setPathParams(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
setPaths(List<DerivePath>) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles: All files need to be present
setPaths(StringSet) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
setPenaltyValue(double) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
setPeriodTriggerBank(PeriodTriggerBank<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
setPermutation(AnchorBean<?>, Object) - Method in interface org.anchoranalysis.bean.permute.setter.PermutationSetter
setPermutation(AnchorBean<?>, Object) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterList
setPermutation(AnchorBean<?>, Object) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
setPermutation(PermuteProperty<S>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A permutation to apply.
setPermutations(List<PermuteProperty<S>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: A list of permutations to apply.
setPermuteProperty(PermuteProperty<?>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
setPermuteProperty(PermuteProperty<Integer>) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
setPermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
setPhysical(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
setPlotBackgroundColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
setPlotGridlineColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
setPoint(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
setPointConnectedComponentID(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
setPointDirection(Point3i, int, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
setPoints(Point3d, Point3d) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
setPoints(Point3i, Point3i) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
setPointsFitter(String) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy: Name of the PointsFitter to use.
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
setPointsFitter(PointsFitterToMark) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
setPointsFitter(PointsFitterToMark) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
setPointsFromOrientationProposer(PointsFromOrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
setPointsFromOrientationXYProposer(PointsFromOrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
setPointsProposer(PointsProposer) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
setPos(Point3d) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
setPositionProposer(PositionProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
setPositionProposer(PositionProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
setPower(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
setPrefix(boolean) - Method in class org.anchoranalysis.bean.define.adder.FromXmlList: If true, a prefix is prepended to the name of each added bean.
setPrefix(String) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean: A prefix that is placed before the name of every bean created
setPrefix(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
setPrefix(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
setPrependColor(RGBColorBean) - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend
setPrependString(String) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
setPrependString(String) - Method in class org.anchoranalysis.feature.bean.list.PrependName
setPrependString(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
setPrependString(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
setPreserveExtensionIfDuplicate(boolean) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions: Keeps the extension if the file-name (without the extension) becomes duplicated with another
setProbMapID(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
setProbNeg(double) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
setProbPos(double) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
setProperty(String, Object) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
setPropertyPath(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath: Either a direct property of a bean e.g.
setProposal(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
setProposer(MarkFromCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
setProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
setProvider(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
setPxlPartMemo(MemoCollection) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
setPxlPartMemo(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
setQuantile(double) - Method in class org.anchoranalysis.feature.bean.results.Quantile: The quantile.
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
setQuantileHigh(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
setQuantileLow(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
setQuantileLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
setQuantileUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
setRadiiProposer(RadiiProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
setRadiiProposer(RadiiProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
setRadius(double) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
setRadius(double) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
setRadius(int) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
setRadius(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
setRadiusBound(Bound) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
setRadiusBound(Bound) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
setRadiusInMeters(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
setRadiusX(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
setRadiusY(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
setRadiusZ(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
setRate(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
setReceive(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
setRecurseSubfolders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
setRecursive(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: Whether to apply the search recursively or not
setRed(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
setRed(int) - Method in class org.anchoranalysis.core.color.RGBColor
setRed(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
setReduce(FeatureListElem<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair: Method for reducing all pairs into a single value e.g.
setReduce(ReduceElements<ObjectMask>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima: The algorithm for reducing the number of object-masks.
setReferencePoissonIntensity(double) - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
setReferencesFeatureListCreator(StringSet) - Method in class org.anchoranalysis.feature.bean.list.ReferencedFeatures: Ensures any feature-lists mentioned here are evaluated, before this list is created.
setReferencesFeatureListCreator(StringSet) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature: Makes sure a particular feature list creator is evaluated
setRegex(String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
setRegex(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: Regular expression to match against string
setRegex(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: A regular-expression applied to the image file-path that matches three groups.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx: Regular expression to use to match path with at least one group in it.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: The regular-expression to use for matching groups.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching: If a path matches a regular expression it is removed.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
setRegexAdjacent(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: This needs to be set if there is at least one adjacentChannel.
setRegExDir(String) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to directories
setRegExFile(String) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to files
setRegExString(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: The regular-expression to use for matching groups, overloaded to handle legacy situations where a string is supplied.
setRegion(MarkRegion) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
setRegion(MarkRegion) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
setRegionID(int) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.FeatureMarkRegion
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
setRegionID(int) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
setRegionMap(RegionMap) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
setRejectIterationIfAllLow(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
setRejectIterationIfDisconnected(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
setRelation(RelationBean) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs: Relation to threshold
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
setRemoveExtensionInDescription(boolean) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories: Whether to remove the file-extension from the filename.
setRemoveTouchingBorderXY(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
setRepeat(int) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
setRepeats(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth: Total number of births
setReplaceMatchesWithSolids(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
setReplacement(String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
setReplacement(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: What to replace in the path
setReplacement(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile: The replacement string used to determine the file
setReplaceWithMidpoint(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
setReportFitterErrors(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
setRequireAllFilesMatch(boolean) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
setRequireArguments(RequireArguments) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf: The conditions that must be fulfilled
setRequireArguments(RequireArguments) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
setRequireBBoxNeighbors(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch
setRequireTouching(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature: Requires the object-masks to touch.
setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask: If set, each channel is scaled to a specific size before the mean is calculated (useful for combining different sized images)
setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor: The input-image is rescaled to this width/height before calculating HOG descriptors
setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature: The input is rescaled to this width/height before calculating HOG descriptors
setRestrictTo(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert: If set, the inversion only occurs on a particular region of the mask, as determined by this mask
setResX(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
setResY(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
setResZ(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
setRewardHigherSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore: Treat the higher side as if it's the the fill cdf
setRewardLowerSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
setRgb(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask: If true, the output contains three channels (the input and two duplicates) instead of one
setRoot1(double) - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
setRoot2(double) - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
setRootInStructure(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: If true the directory structure is ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
setRootName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: If non-empty then a rooted filesystem is used with this root
setRootName(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: Root-name assuming multi-rooted strucutre
setRootName(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
setRootNameForStructure(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: If rootInStructure==true, the rootName is placed in the folder structure.
setRotateOnlyIn2DPlane(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
setRotationAngle(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
setRotationAngle(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
setRotationBounds(RotationBounds3D) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
setRotationX(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
setRotationY(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
setRotationZ(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
setRotMatrix(DoubleMatrix2D) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
setRow(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
setSampleEvery(int) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
setScalarProposer(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
setScalarProposer(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
setScale(double) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic: Standard-Deviation
setScale(double) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Whether to increase or reduce the size of the images
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY: Determines how much to scale by
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
setScaleFactor(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
setScaleLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity: Sets the min by multiplying the quantileLower by this constant.
setScaleLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
setScaleRadii(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
setScaleUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity: Sets the max by multiplying the quantileUpper by this constant.
setScaleUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
setScore(VoxelScore) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
setScoreProvider(FeatureListProvider<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
setScoreThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression: Bounding boxes with scores above this threshold are removed
setSecond(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: Only relevant if time==true.
setSecond(List<NamedBean<StringSet>>) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify: Output-names in the second-level (for all first level output-names)
setSecond(StateTransformerBean<U, T>) - Method in class org.anchoranalysis.mpp.segment.transformer.Compose: Second transformation from U to T
setSecondary(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter: If proposal is true, this toggles between the primary and secondary proposal
setSecondary(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel: Segmentation algorithm
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
setSegment(SegmentIntoMarks) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage: How to perform the segmentation.
setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The segmentation procedure.
setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The segmentation algorithm
setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima: The segmentation algorithm that is applied as an input to non-maxima suppression.
setSegmentStack(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
setSelect(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair: Either "merged" or "first" or "second" indicating which feature to delegate from
setSelectChannels(FromStacks) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Selects which channels are included, optionally renaming.
setSeperator(String) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
setSeperator(String) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setSequence(SequenceInteger) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence: Where the sequence starts
setSequence(SequenceInteger) - Method in class org.anchoranalysis.feature.bean.list.ListSequence: First number range that is appended
setSequence(OutputSequenceIndexed<T, S>) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
setSequenceAdditional(SequenceInteger) - Method in class org.anchoranalysis.feature.bean.list.ListSequence: Another number range that is appended
setShellRad(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
setShellRad(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
setShellRad(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setShellRad(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
setShellRad(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
setShellRad(double) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
setShellRad(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
setShift(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
setShowAgg(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
setShowBest(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
setShowDomainAxis(boolean) - Method in class org.anchoranalysis.plot.index.BarPlot
setShowOngoingJobsLessThan(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor: When the number of ongoing jobs is less than this threshold, they are shown in event logs.
setShowVerticalAxisLines(boolean) - Method in class org.anchoranalysis.plot.PlotInstance
setSigma(double) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
setSigma(double) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
setSigmaInMeters(boolean) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
setSilentlyDeleteExisting(boolean) - Method in class org.anchoranalysis.io.output.bean.OutputManager: Whether to silently first delete any existing output at the intended path, or rather throw an error.
setSilentlyDeleteExisting(boolean) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
setSimplePairCollectionID(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
setSize(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
setSize(int) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram: Size of the image produced showing a plot of the histogram
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize: Size of all created thumbnails
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
setSkipAtBorder(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles: If true we do not fill any objects that touch the border
setSkipFileName(boolean) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories: Iff true the filename is not considered, only the subdirectories.
setSkipFileName(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
setSkipFirstTrim(int) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
setSkipFirstTrim(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
setSkipMissingChannels(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setSkipNumberSubdirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories: Initially skip this number of directories before including them in the description.
setSlice(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
setSliceEnd(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
setSliceFirst(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: First slice.
setSliceID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase: Index of slice to use, or -1 to use all slices
setSliceIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice: Which slice to use from mask
setSliceLast(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices: Last slice.
setSliceNum(Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
setSlicesSeparately(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
setSliceStart(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
setSmoothingFactor(double) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
setSource(String) - Method in class org.anchoranalysis.bean.shared.StringMapItem
setSource(FeatureSource<T, S, U>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Source of feature-values to be exported
setSourceFolderPath(FilePath) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
setSplitDescriptiveNameRegex(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
setSplitProposer(MarkSplitProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
setSquareSize(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
setStack(Provider<Stack>) - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
setStack(StackProvider) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV: The stack that is the background for our objects
setStack(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
setStack(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
setStack(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Provides a stack.
setStack(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack: The stack to segment
setStackAsChannel(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick: If true, a raster-stack is treated as a single-channel, even if multiple exist (and no additionalChannel is set)
setStackBackground(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
setStackEnergy(Provider<Stack>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Optionally specifies an energy-stack to be associated with every calculation input.
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks)
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
setStackID(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
setStackName(String) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One: If defined, processing only occurs the stack with this specific stack and index.
setStackNameVisualOriginal(String) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
setStackProviderID(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack: Specifies the ID of an existing stack.
setStackProviderID(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
setStackReader(StackReader) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
setStackReader(StackReader) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: The raster-reader for reading the main file
setStackReaderAdjacent(StackReader) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick: The raster-reader to use for opening any adjacent-channels
setStackReaderAppend(StackReader) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase: The raster-reader for reading any appended files
setStackReaderHigh(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
setStackReaderInput(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
setStackReaderLow(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
setStackReaderMiddle(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
setStacksOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled: Deprecated.

What's allowed or not when outputting stacks
setStacksOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
setStart(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger: The index to begin iteration from
setStartIndex(int) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
setStartingIntensity(int) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel: The first intensity-value to consider as a valid object (e.g.
setStateReporter(StateReporter<T, S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
setStrategy(BlurStrategy) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
setStrongEdgeEnhancer(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion: Enables the StrongEdgeEnhancer diffusion function
setSubdirectory(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure: If non-empty than an additional subdirectory is appended as a suffix ${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
setSubDirectory(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
setSubtractConstant(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
setSubtractFromMaskOnly(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
setSubtractRadii(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
setSuffix(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
setSummarizer(Summarizer<S>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
setSummarizer(Summarizer<S>) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
setSummarizerElse(Summarizer<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) <= countThreshold
setSummarizerGreaterThan(Summarizer<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) > countThreshold
setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
setSuppressErrors(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
setSuppressExceptions(boolean) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
setSuppressExceptions(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
setSuppressExceptions(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
setSuppressOutlineZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase: if true, the outline is suppressed in the z-dimension i.e.
setSuppressRes(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
setSuppressRootOut(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML.
setSuppressSeries(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: If true, the series index is not included in the outputted file-names.
setSuppressSubfolders(boolean) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
setSuppressZ(boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: If true co-voariance is suprpessed in z-dimension
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase: Iff true, surpresses covariance in the z-direction.
setSuppressZCovariance(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
setSuppressZCovariance(boolean) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
setTarget(String) - Method in class org.anchoranalysis.bean.shared.StringMapItem
setTask(Task<MultiInput, S>) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
setTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
setTask(Task<T, S>) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
setTask(Task<T, S>) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
setTask(Task<U, S>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
setTask(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
setTaskName(Optional<String>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments: A name to describe the ongoing task
setTaskProcessor(JobProcessor<T, S>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment: What task is associated with the experiment, and how it is processed.
setTemperature(double) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
setTemplateMark(MarkFactory) - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
setTermination(TerminationCondition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
setThreshold(double) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
setThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
setThreshold(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold: Only considers values greater or equal to the threshold
setThreshold(double) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
setThreshold(double) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
setThreshold(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
setThreshold(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
setThreshold(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
setThreshold(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
setThreshold(UnitValueVolume) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
setThresholder(Thresholder) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
setThresholder(Thresholder) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold: The thresholder that will convert a channel into a binary-channel
setThresholdHigh(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
setThresholdLow(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
setThrowExceptionForInsufficientPoints(boolean) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
setThumbnail(ThumbnailFromObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Generates a thumbnail representation of one or more objects combine, as form a single input
setThumbnail(ThumbnailFromStack) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Method to generate a thumbnail for images
setTime(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto: If true, the current time (HH.mm.ss) is included in the output
setTimeIndex(int) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
setTimeIndex(Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
setTimeIndexGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
setTimes(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat
setTitle(String) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
setTitle(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
setToleranceLog10(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
setTransformer(StateTransformerBean<MarkCollection, T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
setTransformerKernelToState(StateTransformerBean<U, T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
setTransformerMarks(StateTransformerBean<MarkCollection, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
setTransformerPrimary(StateTransformerBean<T, S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
setTransformerSecondary(StateTransformerBean<T, S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
setTransformerStateToKernel(StateTransformerBean<T, U>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
setTransposed(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setTrimTrailingDirectory(int) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
setTrimTrailingDirectory(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
setUniqueLabel(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Label that uniquely identifies the ID (for machine purposes)
setUnit(UnitConverter) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
setUnit(UnitConverter) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
setUnitType(String) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
setUnitType(String) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
setUnitTypeFrom(String) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
setUnitTypeTo(String) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
setUnitValueDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo: Always called before any batch of calls to ConvertTo.convertSliceOfSingleChannel(java.nio.ByteBuffer, int).
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
SetUpdatable - Class in org.anchoranalysis.mpp.bean.points.updatable
SetUpdatable() - Constructor for class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
setupParams(KeyValueParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
setupParams(KeyValueParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
setUseLastSeriesIndexOnly(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
setUseLastSeriesIndexOnly(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
setUseMax(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
setUseMax(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
setUseMIP(boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
setUseMIP(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
setUserFriendlyLabel(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel: Descriptive user-friendly label displayed via GUI
setUseZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
setUseZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
setValue(double) - Method in class org.anchoranalysis.feature.bean.operator.Constant
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
setValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
setValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
setValue(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
setValue(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
setValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
setValue(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
setValue(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
setValue(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
setValue(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setValue(String) - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
setValue(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
setValue(T) - Method in class org.anchoranalysis.bean.NamedBean
setValue(T) - Method in interface org.anchoranalysis.core.identifier.name.NameValue: Sets the associated value
setValue(V) - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
setValueByDimension(int, double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
setValueByDimension(int, float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
setValueIfEmpty(double) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic: The value to return iff exceptionifEmpty is false
setValueIfTooFewVoxels(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase: A value to return if there are too few voxels (less than MIN_NUM_VOXELS to calculate moments
setValueNoObject(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
setValueNoObjects(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
setValues(StringSet) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
setValues(StringSet) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet: The values of the string-set
setVaryColors(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: If true the colors change for different objects in the image (using a default color set).
setVersion(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
setVerticalAlign(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
setVisitScheduler(VisitScheduler) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
setWeight(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
setWeightBackground(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
setWeightForeground(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
setWeightItem1Greater(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
setWeightItem2Greater(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
setWeightNegative(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
setWeightPositive(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
setWeightWidthDescription(int) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
setWhenDetailed(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging: Logger to use when detailed-logging is on
setWhenEqual(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setWhenNot(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging: Logger to use when detailed-logging is off
setWhenNotEqual(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
setWhenOneOrThreeChannels(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a one or three-channeled image, that is not 3D, and not RGB.
setWhenRGB(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a three-channeled RGB image and is not 3D.
setWidth(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference: Width (what the difference is divided by)
setWidth(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
setWidthFactor(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
setWindowSize(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
setWindowSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: The window-size as per OpenCV implementation.
setWithin(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange: Returned as a constant if a value lies within the range
setWithinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange: Constant to return if value lies within the range
setWithinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature: Constant to return if value lies within the range
setWriter(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Default writer, if a more specific writer is not specified for a condition.
setWriter(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
setWriterAlways2D(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Writer to use if it is guaranteed that the image will always be 2D.
setWriterElse(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Otherwise the writer to use.
setWriters(List<NamedBean<?>>) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings: Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
setX(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
setX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
setX(int) - Method in class org.anchoranalysis.spatial.point.Point2i
setX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
setX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
setX(String) - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
setXY(String, String) - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
setY(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
setY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
setY(int) - Method in class org.anchoranalysis.spatial.point.Point2i
setY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
setY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
setY(String) - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
setYAxisLowerMargin(double) - Method in class org.anchoranalysis.plot.index.LinePlot
setYAxisMargins(double) - Method in class org.anchoranalysis.plot.index.LinePlot
setYAxisUpperMargin(double) - Method in class org.anchoranalysis.plot.index.LinePlot
setYValGetter(LinePlot.YValGetter<T>) - Method in class org.anchoranalysis.plot.index.LinePlot
setZ(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
setZ(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
setZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
setZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
setZAlign(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
setZOnly(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
setZSliceGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
setZSliceNum(int) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
SgmnMPPState - Class in org.anchoranalysis.plugin.mpp.segment
SgmnMPPState(KernelProposer<VoxelizedMarksWithEnergy>, Define) - Constructor for class org.anchoranalysis.plugin.mpp.segment.SgmnMPPState
shallowCopy() - Method in class org.anchoranalysis.core.color.ColorList
shallowCopy() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: Creates a new graph with identical elements and structure, reusing the existing vertice and edge data objects.
shallowCopy() - Method in class org.anchoranalysis.feature.name.FeatureNameList
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Make a shallow copy
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy: Creates a shallow-copy of the marks
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
shallowCopy() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
shallowCopy() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
shallowCopy() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
shallowDuplicate() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Creates a new feature-list which contains identical elements
ShapeRegularityCenterSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
ShapeRegularityCenterSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityCenterSlice
ShapeRegularityMIP - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
ShapeRegularityMIP() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityMIP
SharedFeatureMulti - Class in org.anchoranalysis.feature.shared: A group of features (of possibly heterogeneous type) made available to other features to reference
SharedFeatureMulti() - Constructor for class org.anchoranalysis.feature.shared.SharedFeatureMulti
SharedFeatureSet<T extends FeatureInput> - Class in org.anchoranalysis.feature.shared
SharedFeatureSet(NameValueSet<Feature<T>>) - Constructor for class org.anchoranalysis.feature.shared.SharedFeatureSet
SharedFeaturesInitParams - Class in org.anchoranalysis.feature.shared
SharedObjects - Class in org.anchoranalysis.core.identifier.provider.store: Objects shared between different components.
SharedObjects(CommonContext) - Constructor for class org.anchoranalysis.core.identifier.provider.store.SharedObjects
sharedObjectsRequired() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
SharedStateExportFeatures<S> - Class in org.anchoranalysis.plugin.image.task.feature: Shared-state for an export-features class
SharedStateExportFeatures(ResultsWriterMetadata, Supplier<S>, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures: Creates the shared state.
SharedStateFilteredImageOutput<T> - Class in org.anchoranalysis.plugin.image.task.labeller
SharedStateFilteredImageOutput(Outputter, ImageLabeller<T>) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
SharedStateSegmentInstance<T> - Class in org.anchoranalysis.plugin.image.task.segment: Shared-state for instance segmentation
SharedStateSegmentInstance(ConcurrentModelPool<T>, FeatureTableCalculator<FeatureInputSingleObject>, LabelHeaders, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
SharedStateSelectedSlice - Class in org.anchoranalysis.plugin.image.task.slice
SharedStateSelectedSlice(Outputter) - Constructor for class org.anchoranalysis.plugin.image.task.slice.SharedStateSelectedSlice
Shell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
Shell() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
shift() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: Increments the slice number by one
shiftBackBy(VoxelsAssigner, ReadableTuple3i) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Shifts all coordinates BACKWARDS before passing to another VoxelsAssigner.
shiftBackBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Shifts the object-mask by moving its bounding-box backwards (i.e.
shiftBackBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Shifts the bounding-box backwards.
shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Shifts the bounding-box of each object by adding to it i.e.
shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Shifts the object-mask by moving its bounding-box forwards (i.e.
shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Shifts the bounding-box forwards.
shiftBy(T, ReadableTuple3i) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask: Positionally-shifts an element by a given quantity in the positive direction.
shiftTo(Point3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Assigns a new corner-location to the bounding-box.
shiftToOrigin() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates a new object-mask with identical voxels but with the bounding-box beginning at the origin (0,0,0)
shiftToOrigin() - Method in class org.anchoranalysis.spatial.box.BoundingBox: Moves the bounding-box to the origin (0,0,0) but preserves the extent
shiftToZ(int) - Method in class org.anchoranalysis.spatial.box.BoundingBox: Assigns a new z-slice corner-location to the bounding-box
SHORT_OPTION_DEBUG - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
SHORT_OPTION_HELP - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
SHORT_OPTION_INPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
SHORT_OPTION_LOG_ERROR - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
SHORT_OPTION_OUTPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
SHORT_OPTION_OUTPUT_DISABLE_ADDITIONAL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
SHORT_OPTION_OUTPUT_ENABLE_ADDITIONAL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
SHORT_OPTION_OUTPUT_ENABLE_ALL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
SHORT_OPTION_SHOW_EXPERIMENT_ARGUMENTS - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
SHORT_OPTION_TASK - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
SHORT_OPTION_VERSION - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase: Whether to overwrite the current voxel-value with the constant?
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxWithConstant
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinWithConstant
shuffle() - Method in class org.anchoranalysis.core.color.ColorList
Shuffle - Class in org.anchoranalysis.bean.shared.color.scheme: Randomizes the order of the colors from existing scheme.
Shuffle<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Randomly shuffles the order of an input-manager
Shuffle() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Shuffle
Shuffle() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Shuffle
Shuffle(ColorScheme) - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Shuffle
SignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype
SignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype
SignedVoxelType(int, String, long, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
SimpleAnnotationDeleter - Class in org.anchoranalysis.annotation.io: Deletes any annotation that is only the file represented at the path
SimpleAnnotationDeleter() - Constructor for class org.anchoranalysis.annotation.io.SimpleAnnotationDeleter
SimpleCopy - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
SimpleCopy() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.SimpleCopy
SimpleManifestDeserializer - Class in org.anchoranalysis.io.manifest.deserializer
SimpleManifestDeserializer() - Constructor for class org.anchoranalysis.io.manifest.deserializer.SimpleManifestDeserializer
SimpleName - Class in org.anchoranalysis.feature.io.name: A name with only one part, and is always unique.
SimpleName(String) - Constructor for class org.anchoranalysis.feature.io.name.SimpleName
SimpleNameValue<V> - Class in org.anchoranalysis.core.identifier.name: A simple container expressing a name-value pair
SimpleNameValue(String, V) - Constructor for class org.anchoranalysis.core.identifier.name.SimpleNameValue
SimpleOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
SimpleOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
SimpleOverlayWriter - Class in org.anchoranalysis.mpp.io.marks.generator: Converts a configuration to a set of object-masks, using a simple DrawObject for all objects.
SimpleOverlayWriter(DrawObject) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
SimplePropertyDefiner - Class in org.anchoranalysis.bean.initializable.property
SimplePropertyDefiner(Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
SimulatedAnnealing<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme: Finds an optima using a simulated-annealing approach
SimulatedAnnealing() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
Single - Class in org.anchoranalysis.image.bean.spatial.arrange
Single - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
Single() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Single
Single() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
SingleChannel - Class in org.anchoranalysis.plugin.image.feature.bean.score: A score that is calculated on a single channel only
SingleChannel - Class in org.anchoranalysis.plugin.io.bean.channel.map: For an image with a single channel
SingleChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
SingleChannel() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
SingleChannel(String) - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
SingleColor - Class in org.anchoranalysis.core.color: An index that always uses the same single color
SingleColor(Color) - Constructor for class org.anchoranalysis.core.color.SingleColor
SingleColor(RGBColor) - Constructor for class org.anchoranalysis.core.color.SingleColor
SingleContainer<T> - Class in org.anchoranalysis.core.index.bounded
SingleContainer(boolean) - Constructor for class org.anchoranalysis.core.index.bounded.SingleContainer
SingleContainer(T, int, boolean) - Constructor for class org.anchoranalysis.core.index.bounded.SingleContainer
SingleFileTypeGenerator<T,S> - Class in org.anchoranalysis.io.generator: A Generator that eventually writes only a single file to the filesystem.
SingleFileTypeGenerator() - Constructor for class org.anchoranalysis.io.generator.SingleFileTypeGenerator
SingleFileTypeGeneratorBridge<S,T,V> - Class in org.anchoranalysis.io.generator: Allows us to call an SingleFileTypeGenerator<V,S> as if it was an SingleFileTypeGenerator<T,S> using an function to connect the two.
SingleFileTypeGeneratorBridge(SingleFileTypeGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
SingleLevelAnd - Class in org.anchoranalysis.io.output.enabled.single: Outputs are enabled if they are contained in both of two SingleLevelOutputEnabled.
SingleLevelAnd(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelAnd: Creates using two SingleLevelOutputEnableds.
SingleLevelBinary - Class in org.anchoranalysis.io.output.enabled.single: Base class for a SingleLevelOutputEnabled that combines two existing such classes.
SingleLevelBinary(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary
SingleLevelInSet - Class in org.anchoranalysis.io.output.enabled.single: Outputs are enabled if they are contained in a set.
SingleLevelInSet(Set<String>) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelInSet
SingleLevelNot - Class in org.anchoranalysis.io.output.enabled.single: The complement of an existing SingleLevelOutputEnabled where disabled outputs are enabled, and vice-versa.
SingleLevelNot(SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelNot
SingleLevelOr - Class in org.anchoranalysis.io.output.enabled.single: Outputs are enabled if they are contained in either of two SingleLevelOutputEnabled.
SingleLevelOr(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelOr: Creates using two SingleLevelOutputEnableds.
SingleLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.single
SingleMarkProvider - Class in org.anchoranalysis.mpp.bean.provider: Provides (maybe) a single mark
SingleMarkProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.SingleMarkProvider
SingleObjectFromChannelFactory - Class in org.anchoranalysis.image.core.object.factory
SingleObjectFromPointsFactory - Class in org.anchoranalysis.image.core.object.factory
SinglePathStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
SinglePathStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
singleProcessor(int) - Static method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan: Creates a plan for a single-CPU processor
SingleRowPerInput<T extends InputFromManager,S extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Base class for exporting features, where features are calculated per-image using a NamedFeatureStore.
SingleRowPerInput(String) - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
SingleTableCalculator - Class in org.anchoranalysis.image.feature.session
SingleTableCalculator(NamedFeatureStore<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.session.SingleTableCalculator
size() - Method in class org.anchoranalysis.core.color.ColorList
size() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
size() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
size() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
size() - Method in class org.anchoranalysis.feature.name.FeatureNameList
size() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
size() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
size() - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements: Number of scaled-elements.
size() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
size() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
size() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
size() - Method in class org.anchoranalysis.image.core.stack.NamedStacks: Number of stacks
size() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
size() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
size() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
size() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
size() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
size() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
size() - Method in class org.anchoranalysis.math.histogram.Histogram: The number of items in the histogram (maxBin - minBin + 1)
size() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
size() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
size() - Method in class org.anchoranalysis.mpp.bean.points.updatable.UpdatablePointsContainer
size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
size() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
size() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
size() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
size() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
size() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
size() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
size() - Method in interface org.anchoranalysis.mpp.mark.voxelized.memo.MemoForIndex
size() - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
size() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
size() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
size() - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
size() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
size() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
size() - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
size() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
size() - Method in class org.anchoranalysis.spatial.box.BoundedList: The number of elements
size() - Method in class org.anchoranalysis.spatial.rtree.RTree
Size - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
Size() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Size
sizeBytes - Variable in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
sizeCurrentLoad() - Method in class org.anchoranalysis.core.cache.LRUCache: Number of items currently in the cache
sizeCurrentLoad() - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti: Number of items currently in the cache
sizeDescriptor(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters: Calculates the size of the descriptor will be for a given image, assuming the window is equal to the image-size
SizeExtents - Class in org.anchoranalysis.plugin.io.multifile: Remembers the different sizes among the files
SizeExtents(ParsedFilePathBag) - Constructor for class org.anchoranalysis.plugin.io.multifile.SizeExtents
sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
sizeFeatures() - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti: The number of features that is calculated on each call to calc(), and therefore the size of the ResultsVector returned
sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
sizeFeatures() - Method in class org.anchoranalysis.feature.session.SequentialSession
sizeFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
sizeFeatures() - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
sizeFirst() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: The number of elements in the first list.
sizeSecond() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: The number of elements in the second list.
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
sizeXY - Variable in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
SizeXY - Class in org.anchoranalysis.image.bean.spatial
SizeXY() - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY
SizeXY(int, int) - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY
SizeXY(Extent) - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY: Constructor
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
skewness(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics
Skewness - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Skewness() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Skewness
SkipInit - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that this particular bean-field should be ignored during (recursive) initialisation
slice(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
slice(int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
slice(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Creates a new Voxels with only particular slice
slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
slice(int) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
slice(int) - Method in class org.anchoranalysis.image.voxel.Voxels
slice(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
SliceAt - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
SliceAt() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
sliceBuffer(int) - Method in class org.anchoranalysis.image.core.mask.Mask
sliceBuffer(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
sliceBuffer(int) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
sliceBuffer(int) - Method in class org.anchoranalysis.image.voxel.Voxels
sliceBufferGlobal(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A slice buffer with global coordinates
sliceBufferGlobal(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A slice buffer with global coordinates
SliceBufferIndex<T> - Interface in org.anchoranalysis.image.voxel.factory.sliceindex: Provides voxel-buffers for each z-slice.
sliceBufferLocal(int) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
sliceBufferLocal(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A slice buffer with local coordinates i.e.
sliceBufferLocal(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A slice buffer with local coordinates i.e.
slices() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
slices() - Method in class org.anchoranalysis.image.voxel.Voxels
sliceStatisticsForRegion(VoxelizedMark, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
SliceThresholder - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
SliceThresholder(BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
SliceThresholderMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
SliceThresholderMask(boolean, ObjectMask, BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderMask
SliceThresholderWithoutMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
SliceThresholderWithoutMask(BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderWithoutMask
SlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer: Contains the buffer for the current slice, the current slice minus 1, and the current slice plus 1
SlidingBuffer(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
Sobel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: 3x3 Sobel Filter
Sobel() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.Sobel
solveQuadraticEquation(double, double, double) - Static method in class org.anchoranalysis.math.equation.QuadraticEquationSolver: Solves a quadratic equation in form x^2 + b^x + c = 0
sort(Comparator<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Creates a new feature-list sorted in a particular order.
SortAlphabetically<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Sorts the input-items in alphabetical order of their input-name.
SortAlphabetically - Class in org.anchoranalysis.plugin.io.bean.provider.file
SortAlphabetically() - Constructor for class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
SortAlphabetically() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabetically
SortAlphabeticallyWithDirectory - Class in org.anchoranalysis.plugin.io.bean.provider.file
SortAlphabeticallyWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabeticallyWithDirectory
SortByFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Creates a new object-collection with objects sorted by a derived feature-value (in ascending order)
SortByFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.SortByFeature
SortedSetChannel - Class in org.anchoranalysis.plugin.io.multifile
SortedSetChannel() - Constructor for class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
SortedSetSlice - Class in org.anchoranalysis.plugin.io.multifile
SortedSetSlice(String, int) - Constructor for class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
sourceVal - Variable in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
spatiallySeparate() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree: Splits the collection of objects into spatially separate clusters.
SpatiallySeparate<T> - Class in org.anchoranalysis.spatial.rtree
SpatiallySeparate(Function<T, BoundingBox>) - Constructor for class org.anchoranalysis.spatial.rtree.SpatiallySeparate
SpatialUnits - Class in org.anchoranalysis.image.core.dimensions: Units to describe spatial quantities.
SpatialUnits.UnitSuffix - Enum in org.anchoranalysis.image.core.dimensions: Suffix that describes a particular quantity of units (micron, nano, square microns etc.)
Specific - Class in org.anchoranalysis.plugin.mpp.bean.region
Specific() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.Specific
SpecificAndRename - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects a specific set of channels from stacks, each identified by a stack-name and channel index
SpecificAndRename() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
SpecificAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments: A feature based one one-specific principal-axis as identified by image moments.
SpecificAxisBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
SpecificDisabled - Class in org.anchoranalysis.io.output.bean.enabled: Only specific outputs, identified by a textual name, are disabled, and all others are enabled.
SpecificDisabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
SpecificDisabled(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
SpecificEnabled - Class in org.anchoranalysis.io.output.bean.enabled: Only specific outputs, identified by a textual name, are enabled.
SpecificEnabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
SpecificEnabled(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
SpecificEnergyChannelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
SpecificEnergyChannelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
Sphere - Class in org.anchoranalysis.mpp.mark.conic: A sphere
Sphere() - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere
Sphere(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere: Creates with a radius within particular bounds.
Sphere(Sphere) - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere: Copy Constructor
split(Path) - Method in class org.anchoranalysis.bean.shared.path.RootPath: It splits the *root* portion of the path from the remainder
split(Path, String, boolean) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap: Given a path, it splits the *root* portion of the path from the remainder, trying a root identified by the rootName and debugMode (and if this fails, also trying with debugMode==false)
SplitByObjects - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
SplitByObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
SplitContourAtSaddlePoints - Class in org.anchoranalysis.plugin.points.bean.provider.object: Splits a 2D contour represented by an object-mask into several contours, splitting at "turn" points.
SplitContourAtSaddlePoints() - Constructor for class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
SplitContourSmoothingSpline - Class in org.anchoranalysis.plugin.points.bean.contour
SplitIntoSquares - Class in org.anchoranalysis.plugin.image.bean.object.provider.split: Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
SplitIntoSquares() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
SplitPath - Class in org.anchoranalysis.core.system.path: A path that has been split into two components: a root and a remainder.
SplitPath(Path, Path) - Constructor for class org.anchoranalysis.core.system.path.SplitPath
SQUARE_MICRO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
SQUARE_NANO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
stack() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
stack(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
Stack - Class in org.anchoranalysis.image.core.stack: One ore more single-channel images that all have the same dimensions.
Stack() - Constructor for class org.anchoranalysis.image.core.stack.Stack
Stack(Stream<Channel>) - Constructor for class org.anchoranalysis.image.core.stack.Stack
Stack(Channel) - Constructor for class org.anchoranalysis.image.core.stack.Stack
Stack(Channel...) - Constructor for class org.anchoranalysis.image.core.stack.Stack
Stack(Dimensions, ChannelFactorySingleType, int) - Constructor for class org.anchoranalysis.image.core.stack.Stack
StackIdentifiers - Class in org.anchoranalysis.image.experiment.identifiers
StackNotUniformSized - Class in org.anchoranalysis.image.core.stack
StackNotUniformSized() - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized
StackNotUniformSized(Stream<Channel>) - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized
StackNotUniformSized(Channel) - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized
StackProvider - Class in org.anchoranalysis.image.bean.provider.stack
StackProvider() - Constructor for class org.anchoranalysis.image.bean.provider.stack.StackProvider
StackProviderUnary - Class in org.anchoranalysis.image.bean.provider.stack
StackProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
stacks() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
stacks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
Stacks - Class in org.anchoranalysis.plugin.io.bean.input.stack: Each file gives either: * a single stack * a time-series of stacks
Stacks() - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
Stacks(InputManager<FileInput>) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
STACKS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories: Where stacks are typically placed in a define-experiment output
stackTrace() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException: Prints a stack trace of the current exception to a string
StackWithMap - Class in org.anchoranalysis.mpp.io.input: Combines a Stack with a map of other stacks
StackWithMap(String, ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.StackWithMap
standardDeviation() - Method in class org.anchoranalysis.math.histogram.Histogram
StandardDeviation - Class in org.anchoranalysis.feature.bean.results: The standard-deviation of the results from a particular feature.
StandardDeviation() - Constructor for class org.anchoranalysis.feature.bean.results.StandardDeviation
start() - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
start() - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
start() - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
start() - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
start() - Method in interface org.anchoranalysis.experiment.log.StatefulMessageLogger
start() - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
start() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
start() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
start() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack: Should always be called once before any calls to ThumbnailFromStack.thumbnailFor(org.anchoranalysis.image.core.stack.Stack)
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
start(FeatureInitParams, SharedFeatureMulti, Logger) - Method in class org.anchoranalysis.feature.session.SequentialSession: Starts the session
start(EnergyStack) - Method in class org.anchoranalysis.mpp.feature.bean.mark.CheckMark: Called before any calls to CheckMark.check(org.anchoranalysis.mpp.mark.Mark, org.anchoranalysis.mpp.bean.regionmap.RegionMap, org.anchoranalysis.feature.energy.EnergyStack)
start(EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
start(EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
start(ImageInitParams, Optional<EnergyStack>, Logger) - Method in interface org.anchoranalysis.image.feature.session.FeatureTableCalculator: Initializes a feature store that has the same structure as that previously created by createFeatures() from the same object
start(ImageInitParams, Optional<EnergyStack>, Logger) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
start(ImageInitParams, Optional<EnergyStack>, Logger) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.ThumbnailFromObjects: Initializes a batch to create thumbnails.
start(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Derives a list of inputs from an object-collection
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
startSeries(NoSharedState, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
startSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
startSeries(OutputSequenceIncrementing<Stack>, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
startSeries(S, U, InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask: Starts processing of a series.
StatefulMessageLogger - Interface in org.anchoranalysis.experiment.log: A MessageLogger that can be started and stopped, and is aware this state.
StatefulNullMessageLogger - Class in org.anchoranalysis.experiment.bean.log: Does nothing (i.e.
StatefulNullMessageLogger() - Constructor for class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
stateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
stateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
stateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
StateReporter<T,S> - Class in org.anchoranalysis.mpp.segment.bean.optimization: Converts the optimization state to a form that the reporter needs
StateReporter() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.StateReporter
StateReporterIdentity<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter: Assumes the state is reported without any transformation
StateReporterIdentity() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterIdentity
StateReporterToPixelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter: Assumes we are interested in VoxelizedMarksWithEnergy as reporting type, and our optimization-state is in the form ToPixelized<T>
StateReporterToPixelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
StateReporterTransformer<T,S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
StateReporterTransformer() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridge
stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeIdentity
stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
StateTransformer<W,X> - Interface in org.anchoranalysis.mpp.segment.transformer
StateTransformerBean<S,T> - Class in org.anchoranalysis.mpp.segment.transformer: Transforms one type into another
StateTransformerBean() - Constructor for class org.anchoranalysis.mpp.segment.transformer.StateTransformerBean
StaticFilePath - Class in org.anchoranalysis.plugin.io.bean.filepath
StaticFilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
StatisticalScoreBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.score: Calculates a score based upon the statistical mean and std-deviation.
StatisticalScoreBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
StatisticForFeature - Class in org.anchoranalysis.feature.bean.results: Base class for calculating a statistic across all results in a ResultsVectorList for a particular feature.
StatisticForFeature() - Constructor for class org.anchoranalysis.feature.bean.results.StatisticForFeature
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Mean
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Quantile
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.StandardDeviation
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Sum
statisticsFor(int, int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
statisticsForAllSlices(int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
statisticsForAllSlices(VoxelizedMark, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
statisticsForAllSlicesMaskSlice(int, int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
stdDev() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
StdDev - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
StdDev() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.StdDev
Steepest - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
Steepest(SlidingBuffer<?>, WatershedEncoding, boolean, boolean, Optional<ObjectMask>) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.Steepest
steepestDescent(Point3i, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.Steepest
StoreSupplier<T> - Interface in org.anchoranalysis.core.identifier.provider.store: Supplier of an object for a store
strategyForGrandchild() - Method in class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
strategyForGrandchild() - Method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
strategyForGrandchild() - Method in interface org.anchoranalysis.feature.session.strategy.child.FindChildStrategy: What strategy to use for children-of-children?
stream() - Method in class org.anchoranalysis.core.functional.StreamableCollection
stream() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
stream() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
stream() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Provides various functional-programming operations on the object-collection
stream() - Method in class org.anchoranalysis.spatial.box.BoundedList: A stream of elements in the list.
StreamableCollection<T> - Class in org.anchoranalysis.core.functional: As a stream can only be used once, this data-structure allows for repeatedly getting streams from a collection
StreamableCollection(Collection<T>) - Constructor for class org.anchoranalysis.core.functional.StreamableCollection: Create for a particular collection
StreamableCollection(Supplier<Stream<T>>) - Constructor for class org.anchoranalysis.core.functional.StreamableCollection
streamOverZ() - Method in class org.anchoranalysis.spatial.Extent: Streams over the range of z values
streamStandardJava() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: A stream of object-masks as per Java's standard collections interface
StringBeanCollection - Interface in org.anchoranalysis.bean: A bean that provides a collection of Strings.
StringGenerator - Class in org.anchoranalysis.io.generator.text
StringGenerator() - Constructor for class org.anchoranalysis.io.generator.text.StringGenerator
StringList - Class in org.anchoranalysis.bean: A list of strings (order is defined).
StringList() - Constructor for class org.anchoranalysis.bean.StringList
StringListFactory - Class in org.anchoranalysis.bean.xml.factory: Creates a StringList from a XML element.
StringListFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.StringListFactory
StringMap - Class in org.anchoranalysis.bean.shared
StringMap() - Constructor for class org.anchoranalysis.bean.shared.StringMap
StringMapItem - Class in org.anchoranalysis.bean.shared: A simple mapping from one string (source) to another (target)
StringMapItem() - Constructor for class org.anchoranalysis.bean.shared.StringMapItem
stringRepresentationForElement(int) - Method in interface org.anchoranalysis.io.manifest.sequencetype.IncompleteElementRange: Returns the typed-index corresponding to the integer-index.
StringSet - Class in org.anchoranalysis.bean: A set of strings.
StringSet() - Constructor for class org.anchoranalysis.bean.StringSet
StringSet(String...) - Constructor for class org.anchoranalysis.bean.StringSet
StringSetFactory - Class in org.anchoranalysis.bean.xml.factory: Creates a StringSet from a XML element.
StringSetFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.StringSetFactory
StringSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
StringSuffixOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
StringSuffixOutputNameStyle(String, Optional<String>) - Constructor for class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
StringsWithoutOrder - Class in org.anchoranalysis.io.manifest.sequencetype: A sequence of strings that has no order.
StringsWithoutOrder() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
strMarks() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
strPos() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
subdirectories() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory: The MutableDirectory in the manifest for any subdirectories.
subdirectory(String, ManifestDirectoryDescription, boolean) - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext: Creates a new context that writes instead to a subdirectory.
Subdirectory - Class in org.anchoranalysis.io.manifest.directory: A SubdirectoryBase entry in the manifest for a subdirectory.
Subdirectory() - Constructor for class org.anchoranalysis.io.manifest.directory.Subdirectory
Subdirectory(Path) - Constructor for class org.anchoranalysis.io.manifest.directory.Subdirectory
SubdirectoryBase - Class in org.anchoranalysis.io.manifest.directory
SubdirectoryBase() - Constructor for class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
SubdirectoryBase(Path) - Constructor for class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: An optional subdirectory where the group outputs are placed.
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
subList(int, int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
SUBMARK_CORE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
SUBMARK_CORE_INNER - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
SUBMARK_INSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
SUBMARK_OUTSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
SUBMARK_SHELL - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
SUBMARK_SHELL_OUTSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
SubmittedJob - Class in org.anchoranalysis.experiment.task.processor
SubmittedJob(JobDescription, JobState) - Constructor for class org.anchoranalysis.experiment.task.processor.SubmittedJob
subset(StringSet) - Method in class org.anchoranalysis.image.core.stack.NamedStacks: Creates a new collection containing only items whose keys exist in a particular set
subsetCompatibleWith(Class<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti: Extracts the subset of inputs that are compatible with a particular input-type
subsetWhereBBoxIntersects(Dimensions, int, List<BoundingBox>) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
subsetWhereBBoxIntersects(Dimensions, DrawOverlay, List<BoundingBox>) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
subtract(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
subtract(VarianceCalculator) - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
subtract(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
subtract(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i
subtract(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
subtractBackground(Channel, int, boolean) - Static method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor
subtractFrom(int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Subtracts all current voxel-values from a constant-value
SubtractFrom<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
SubtractFrom() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
SubtractFromConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
SubtractFromConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractFromConstant
subtractFromMaxValue() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
SubtractMean - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic: Subtract the mean (of the entire channel or a masked portion thereof) from every voxel
SubtractMean() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
SubtractReducedFromMerged - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair: Calculates merged - reduce(first,second) for a FeatureInputPairObjects
SubtractReducedFromMerged() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.SubtractReducedFromMerged
SubtractSecondFromFirst - Class in org.anchoranalysis.image.feature.bean.object.pair: Subtract second-object from first-object in a pair
SubtractSecondFromFirst() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.SubtractSecondFromFirst
SubtractTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
SubtractTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractTwoChannels
suffixStringForMeters(SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits: A string that describes the suffix for meters.
sum() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
sum() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
sum() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
sum() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
Sum<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
Sum - Class in org.anchoranalysis.feature.bean.results: The sum of the results from a particular feature.
Sum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Sum() - Constructor for class org.anchoranalysis.feature.bean.operator.Sum
Sum() - Constructor for class org.anchoranalysis.feature.bean.results.Sum
Sum() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Sum
Sum(FeatureList<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.Sum
sumBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
summarize() - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException: This summarize() option just looks for the most deep exception that can be 'combined' and takes its message
summarize() - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
summarize() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
summarize() - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
SummarizeBase<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.task
SummarizeBase() - Constructor for class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
summarizeDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: A comma-separated string of all output-names that were not enabled.
summarizeEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: A comma-separated string of all output-names that were enabled.
summarizeIgnoreIdenticalFilePath(Path) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException: If there is no nested-set of combinable exceptions, and the filenameDscr related to this current exception, is identical as the passed parameter, then we simply ignore the LocalisedBean and promote its getCause()
SummarizeInputs<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.task
SummarizeInputs() - Constructor for class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
summarizeMultiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs: Multiplex between RecordedOutputs.summarizeEnabled() and RecordedOutputs.summarizeDisabled().
Summarizer<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Summarizes a set of elements by outputting a descriptive string
Summarizer() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer
SummarizerAggregate<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Collects summary data about a set of input files that will eventually be outputted to the user
SummarizerAggregate() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
SummarizerCount<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: A count of the number of inputs.
SummarizerCount() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
SummarizerInputFromManager<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts a particular item from an InputManager for summarization downstream
SummarizerInputFromManager() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
SummarizerListMultiline<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Creates a string where each line is an element (the string representation thereof)
SummarizerListMultiline() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
SummarizerNamedChannels<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image: Summarzes NamedChannelsInput in different ways
SummarizerNamedChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
SummarizerNamedChannelsSimple<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image: A simple summerizer where there's one summary-item per image (series are ignored!)
SummarizerNamedChannelsSimple() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannelsSimple
SummarizerSplitMoreThan<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Multiplexes between two summarizers depending on the total number of count
SummarizerSplitMoreThan() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
SummaryException - Exception in org.anchoranalysis.core.exception.combinable: A special kind of exception that represents a summary of an existing set of exceptions
SummaryException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.combinable.SummaryException
summaryStr() - Method in class org.anchoranalysis.spatial.Contour
sumNonZero() - Method in class org.anchoranalysis.math.histogram.Histogram
sumOfSquares() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
sumOfSquares() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
sumOfSquares() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
sumOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
SupportsTimeSeries - Class in org.anchoranalysis.io.imagej.bean.stack.writer: Base class for ImageJRasterWriter that does support writing time-series as a stack.
SupportsTimeSeries() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.SupportsTimeSeries
suppressedLogErrorReporter() - Static method in class org.anchoranalysis.test.LoggingFixture: A Logger that doesn't output anything
suppressedLogReporter() - Static method in class org.anchoranalysis.test.LoggingFixture: A MessageLogger that doesn't output anything
SuppressNonMaxima<T> - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack: Applies a segmentation procedure followed by non-maxima suppression.
SuppressNonMaxima() - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
SuppressNonMaxima(SegmentStackIntoObjectsPooled<T>) - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima: Creates with a particular segmentation algorithm as an input.
SuppressNonMaxima(SegmentStackIntoObjectsPooled<T>, ReduceElements<ObjectMask>) - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
SurfaceNumberVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface: The number of voxel-faces along the surface (the faces of each voxel that touch outside)
SurfaceNumberVoxelFaces() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelFaces
SurfaceNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface: The number of voxels on the surface (all voxels on the exterior of the object)
SurfaceNumberVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxels
SurfaceNumberVoxelsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
SurfaceNumberVoxelsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
SurfaceSizeMaskNonZero - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
SurfaceSizeMaskNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
SwitchChannelTime - Class in org.anchoranalysis.io.bioformats.bean.options: Treats the channel index as if it's time, and vice versa
SwitchChannelTime() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
SwitchDetailedLogging - Class in org.anchoranalysis.experiment.bean.log: Switches between two log-reporters depending on whether detailed logging is switched on or not
SwitchDetailedLogging() - Constructor for class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging

T

TableItemArrangement<T> - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange
TableItemArrangement(TableItemArrangement.TableCreator<T>, int, int) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
TableItemArrangement.TableCreator<T> - Interface in org.anchoranalysis.image.bean.nonbean.spatial.arrange
TableItemException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange
TableItemException(Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemException
TableItemException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemException
tail() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
Task<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.task: A task which performs some kind of processing on a specific input-object
Task() - Constructor for class org.anchoranalysis.experiment.bean.task.Task
TaskFactory - Class in org.anchoranalysis.launcher.executor.selectparam.task: A factory that creates SelectParam<Optional<Path>> as required for tasks.
TaskStatistics - Class in org.anchoranalysis.experiment.task: Maintains statistics on the execution of a task (considering jobs in aggregate)
TaskStatistics(long, RunningSum, RunningSum) - Constructor for class org.anchoranalysis.experiment.task.TaskStatistics
TaskWithoutSharedState<T extends InputFromManager> - Class in org.anchoranalysis.experiment.bean.task: A particular type of task that doesn't share-state between running jobs
TaskWithoutSharedState() - Constructor for class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
TerminationCondition - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination: A test on whether to terminate the optimization or not
TerminationCondition() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationCondition
TerminationConditionListOr - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination
TerminationConditionListOr() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
TerminationConditionListOr(TerminationCondition, TerminationCondition) - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
test(byte, byte) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes: Do the combination of two arguments fulfill the predicate?
test(Point3i, T, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.buffer.PredicateBufferBinary: Tests a voxel location in two buffers
test(T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedPredicate: Applies a predicate like with Predicate.test(T).
TestDataInitException - Exception in org.anchoranalysis.test: An exception thrown when test-data cannot be loaded
TestDataInitException(String) - Constructor for exception org.anchoranalysis.test.TestDataInitException
TestDataInitException(Throwable) - Constructor for exception org.anchoranalysis.test.TestDataInitException
TestDataLoadException - Exception in org.anchoranalysis.test: An exception thrown when test-data cannot be loaded
TestDataLoadException(String) - Constructor for exception org.anchoranalysis.test.TestDataLoadException
TestDataLoadException(Throwable) - Constructor for exception org.anchoranalysis.test.TestDataLoadException
TestLoader - Class in org.anchoranalysis.test: Loads test data, which is found at some location on the filesystem
TestLoaderMPP - Class in org.anchoranalysis.test.experiment
TestLoaderMPP(TestLoader) - Constructor for class org.anchoranalysis.test.experiment.TestLoaderMPP
testManifestExperiment(String) - Method in class org.anchoranalysis.test.TestLoader
textColor() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
textColor() - Method in class org.anchoranalysis.core.color.RGBColor
TextFile - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
TextFile() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
TextFileAsIntegerFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
TextFileAsIntegerFromManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromManifest
TextFileAsIntegerFromPath - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
TextFileAsIntegerFromPath() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromPath
TextFileMarksReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
TextFileMarksReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
TextFileMessageLogger - Class in org.anchoranalysis.experiment.log: Logs messages to a text-file.
TextFileMessageLogger(String, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.log.TextFileMessageLogger: Constructs a logger that (always) writes messages to a text-file with a specific path.
TextFileMessageLogger(String, OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.log.TextFileMessageLogger: Constructs a logger that (maybe) writes messages to a text-file, with a path based upon an output name applied to a OutputterChecked.
TextFileOutput - Class in org.anchoranalysis.io.generator.text: Utility for writing to a text-file at a particular path, but only if it is enabled.
TextFileOutput(String) - Constructor for class org.anchoranalysis.io.generator.text.TextFileOutput
TextFileOutputter - Class in org.anchoranalysis.io.generator.text: Maybe creates a TextFileOutput based upon settings in a OutputterChecked.
TextFileReader - Class in org.anchoranalysis.io.manifest.file
TextureScore - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity: From Page 727 from Lin et al (A Multi-Model Approach to Simultaneous Segmentation and Classification of Heterogeneous Populations of Cell Nuclei
TextureScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
ThreeChannels - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
ThreeChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
ThreeColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color: Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.
ThreeColoredObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
ThreeWayBranchXYResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Takes the XY-resolution determined by stackReaderInput.
ThreeWayBranchXYResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
threshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
threshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold: The threshold-value
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
threshold(RelationToThreshold) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
threshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
threshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
threshold(VoxelsWrapper) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder: Like Thresholder.threshold(VoxelsWrapper) but using default binary-values.
threshold(VoxelsWrapper, BinaryValuesByte) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder: Like Thresholder.threshold(VoxelsWrapper, BinaryValuesByte, Optional, Optional) applying the thresholding to the entire set of voxels.
threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder: Thresholds voxels (across a range of values) so that they have only binary range (i.e.
threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
threshold(RelationToValue, double) - Method in class org.anchoranalysis.math.histogram.Histogram
Threshold - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment: Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel if possible.
Threshold() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
ThresholdAgainstChannel - Class in org.anchoranalysis.plugin.image.bean.segment.binary: Thresholds each voxels by comparing against another channel that has per-voxel thresholds
ThresholdAgainstChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
ThresholdConfidence - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce: Combines object-masks by projecting the maximum confidence-level for each voxel and thresholding.
ThresholdConfidence() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
ThresholdConfidence(double) - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence: Creates with a minimum-confidence level.
Thresholded - Class in org.anchoranalysis.plugin.mpp.bean.region
Thresholded() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
ThresholdedFeature - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only keeps objects whose feature-value satisfies a condition relative to a threshold.
ThresholdedFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
ThresholdedVolume - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only keeps objects whose feature-value satisfies a condition relative to a threshold.
ThresholdedVolume() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
Thresholder - Class in org.anchoranalysis.image.bean.threshold: Thresholds a voxels to create a binary-voxels
Thresholder() - Constructor for class org.anchoranalysis.image.bean.threshold.Thresholder
ThresholderAutoIJ - Class in org.anchoranalysis.plugin.fiji.bean.threshold
ThresholderAutoIJ() - Constructor for class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
ThresholderGlobal - Class in org.anchoranalysis.image.bean.threshold: Performs global thresholding.
ThresholderGlobal() - Constructor for class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
ThresholderGlobal(CalculateLevel) - Constructor for class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
ThresholderSimpleFillHoles2D - Class in org.anchoranalysis.plugin.imagej.bean.threshold
ThresholderSimpleFillHoles2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
ThresholderSimpleFillHoles2D(int) - Constructor for class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
thresholdForLevel(Voxels<UnsignedByteBuffer>, int, BinaryValuesByte) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder
thresholdForLevel(VoxelsWrapper, int, BinaryValuesByte, Optional<ObjectMask>, boolean) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder
ThresholdHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold: Thresholds the histogram (using a weightedOtsu) and then applies a feature to the thresholded version
ThresholdHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
ThumbnailBatch<T> - Interface in org.anchoranalysis.plugin.image.thumbnail: Creates thumbnails for a particular batch of objects that can be calibrated to have similar properties (identical scale etc.)
thumbnailFor(Stack) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
thumbnailFor(Stack) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack: Creates a thumbnail for a stack
thumbnailFor(T) - Method in interface org.anchoranalysis.plugin.image.thumbnail.ThumbnailBatch: Creates a thumbnail for an element in the batch
ThumbnailFromObjects - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object: Creates a thumbnail of one or more objects on a stack by drawing the outline of the objects
ThumbnailFromObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.object.ThumbnailFromObjects
ThumbnailFromStack - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack: Creates a thumbnail from a stack
ThumbnailFromStack() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack
Tiff - Class in org.anchoranalysis.io.imagej.bean.stack.writer: Writes a TIFF image using ImageJ.
Tiff - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats: Writes a stack to the filesystem as a TIFF using the Bioformats library.
Tiff() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
Tiff() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
TiffTimeSeries - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
TiffTimeSeries() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
Tile - Class in org.anchoranalysis.image.bean.spatial.arrange
Tile() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Tile
TimeSequence - Class in org.anchoranalysis.image.core.stack
TimeSequence() - Constructor for class org.anchoranalysis.image.core.stack.TimeSequence
TimeSequence(Stack) - Constructor for class org.anchoranalysis.image.core.stack.TimeSequence
title() - Method in class org.anchoranalysis.io.output.bean.ReportFeature
title() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
title() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
title() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
title() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
title() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
toAll() - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns to all the voxels
toArray() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
toArray(T[]) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
toAWTColor() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
toAWTColor() - Method in class org.anchoranalysis.core.color.RGBColor
toBox(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns to only voxels inside a bounding-box
ToByte - Class in org.anchoranalysis.image.voxel.convert: Base class for conversion to unsigned 8-bit.
ToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert
ToByte() - Constructor for class org.anchoranalysis.image.voxel.convert.ToByte
ToByte() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ToByte
ToByteNoScaling - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to a unsigned 8-bit buffer without scaling any values.
ToByteNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
ToByteScaleByMaxValue - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to a unsigned 8-bit buffer linearly scaling against the maximum constant value.
ToByteScaleByMaxValue(int) - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
ToByteScaleByMinMaxValue - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to a unsigned 8-bit buffer scaling against a the minimum and maximum constant.
ToByteScaleByMinMaxValue(int, int) - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
ToByteScaleByType - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to a UnsignedByteBuffer scaling against the maximum value in each buffer.
ToByteScaleByType() - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteScaleByType
ToByteUpperLowerQuantileIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.convert.histogram
ToByteUpperLowerQuantileIntensity() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
toChannel(ImagePlus, Optional<Resolution>) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertFromImagePlus: Converts an ImagePlus to a Channel.
toCommandLineException() - Method in exception org.anchoranalysis.launcher.executor.selectparam.path.InvalidPathArgumentException
ToConsole - Class in org.anchoranalysis.experiment.bean.log: Logs messages to the console.
ToConsole() - Constructor for class org.anchoranalysis.experiment.bean.log.ToConsole
toEitherTwoObjects(ObjectMask, ObjectMask, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels to a value if the position is ON in either of two masks
toExtent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
toFloat() - Method in class org.anchoranalysis.spatial.point.Point2d
ToFloat - Class in org.anchoranalysis.image.core.channel.convert
ToFloat - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat
ToFloat() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToFloat
ToFloat() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
ToFloatNoScaling - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to a FloatBuffer without scaling any values.
ToFloatNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
ToInt - Class in org.anchoranalysis.io.bioformats.copyconvert.toint
ToInt() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toint.ToInt
ToMultiple - Class in org.anchoranalysis.experiment.bean.log: Rather than logging to one location, logs to multiple locations (from a list).
ToMultiple() - Constructor for class org.anchoranalysis.experiment.bean.log.ToMultiple
ToMultiple(LoggingDestination, LoggingDestination) - Constructor for class org.anchoranalysis.experiment.bean.log.ToMultiple: Constructs a logger to two locations
toObject(ObjectMask) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match an object-mask
toObject(ObjectMask, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match a object-mask (but only a part of the object-mask)
toObjectIf(ObjectMask, IntPredicate) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match an object-mask and a voxel matches a predicate
toObjectWhile(ObjectMask, IntPredicate) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match an object-mask and each voxel matches a predicate
toPhysicalArea(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts an area from square voxels to square meters.
toPhysicalArea(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts an area from square voxels to physical units.
toPhysicalDistance(double, DirectionVector) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts a distance from voxels to meters.
toPhysicalDistance(double, DirectionVector, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts a distance from voxels to physical units.
toPhysicalVolume(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts a volume from cubic voxels to cubic meters.
toPhysicalVolume(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter: Converts a volume from cubic voxels to physical units.
ToPixelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization: Before and after state, when a src is coverted in a VoxelizedMarksWithEnergy
ToPixelized(T, VoxelizedMarksWithEnergy) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
ToPixelizedExtracter<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
ToPixelizedExtracter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.ToPixelizedExtracter
toSet() - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Converts to a HashSet (newly-created).
ToShortNoScaling - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to a unsigned 16-bit buffer without scaling any values.
ToShortNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
ToShortScaleByType - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to a unsigned 16-bit buffer, scaling against the maximum value in each data-type.
ToShortScaleByType() - Constructor for class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
toStack(Mat) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertFromMat
toString() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
toString() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
toString() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
toString() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
toString() - Method in class org.anchoranalysis.bean.AnchorBean: By default, we use AnchorBean.describeBean() as the string representation of the bean.
toString() - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
toString() - Method in class org.anchoranalysis.bean.NamedBean
toString() - Method in class org.anchoranalysis.bean.shared.regex.RegExList
toString() - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
toString() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
toString() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
toString() - Method in class org.anchoranalysis.core.color.RGBColor
toString() - Method in exception org.anchoranalysis.core.exception.AnchorRuntimeException
toString() - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
toString() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
toString() - Method in class org.anchoranalysis.core.graph.TypedEdge
toString() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
toString() - Method in class org.anchoranalysis.core.log.CommonContext
toString() - Method in class org.anchoranalysis.core.system.path.SplitPath
toString() - Method in class org.anchoranalysis.core.value.TypedValue
toString() - Method in class org.anchoranalysis.experiment.task.InputTypesExpected
toString() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
toString() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
toString() - Method in class org.anchoranalysis.feature.bean.Feature
toString() - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
toString() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
toString() - Method in class org.anchoranalysis.feature.energy.EnergyTotal
toString() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
toString() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
toString() - Method in class org.anchoranalysis.feature.io.name.CombinedName
toString() - Method in interface org.anchoranalysis.feature.io.name.MultiName: The full name, including both directory and file part, as a string.
toString() - Method in class org.anchoranalysis.feature.io.name.SimpleName
toString() - Method in class org.anchoranalysis.feature.name.FeatureNameList
toString() - Method in class org.anchoranalysis.feature.results.ResultsVector
toString() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
toString() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
toString() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
toString() - Method in class org.anchoranalysis.image.core.channel.Channel: Display a histogram of voxel-intensities as the string-representation
toString() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
toString() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
toString() - Method in class org.anchoranalysis.image.core.mask.Mask
toString() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
toString() - Method in class org.anchoranalysis.image.core.object.MatchedObject
toString() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
toString() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
toString() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
toString() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
toString() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
toString() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
toString() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
toString() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
toString() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
toString() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
toString() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
toString() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
toString() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
toString() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
toString() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
toString() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
toString() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
toString() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Default string representation of the collection, one line with each object described by its center-of-gravity
toString() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A string representation of the object-mask showing: the center-of-gravity the number of "ON" voxels on the object
toString() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
toString() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
toString() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
toString() - Method in class org.anchoranalysis.io.manifest.file.FileType
toString() - Method in class org.anchoranalysis.io.manifest.ManifestDescription
toString() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
toString() - Method in class org.anchoranalysis.io.output.outputter.Outputter
toString() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
toString() - Method in class org.anchoranalysis.launcher.config.HelpConfig
toString() - Method in class org.anchoranalysis.math.histogram.Histogram
toString() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
toString() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
toString() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
toString() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
toString() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
toString() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
toString() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
toString() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
toString() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
toString() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
toString() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
toString() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
toString() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
toString() - Method in class org.anchoranalysis.mpp.mark.Mark: String representation of the mark
toString() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
toString() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
toString() - Method in class org.anchoranalysis.mpp.mark.points.PointList
toString() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
toString() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
toString() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
toString() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
toString() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
toString() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
toString() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
toString() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
toString() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
toString() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
toString() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
toString() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
toString() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
toString() - Method in class org.anchoranalysis.plot.AxisLimits
toString() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
toString() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
toString() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
toString() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
toString() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
toString() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
toString() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
toString() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
toString() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
toString() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
toString() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
toString() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
toString() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
toString() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
toString() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
toString() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
toString() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
toString() - Method in class org.anchoranalysis.spatial.box.BoundingBox
toString() - Method in class org.anchoranalysis.spatial.Extent
toString() - Method in class org.anchoranalysis.spatial.point.Point2d
toString() - Method in class org.anchoranalysis.spatial.point.Point2f
toString() - Method in class org.anchoranalysis.spatial.point.Point2i
toString() - Method in class org.anchoranalysis.spatial.point.Tuple3d
toString() - Method in class org.anchoranalysis.spatial.point.Tuple3f
toString() - Method in class org.anchoranalysis.spatial.point.Tuple3i
toString() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
toString() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
toString(boolean, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: A string representation of all objects in the collection using their center of gravities (and optionally indices)
toStringUnixStyle(String) - Static method in class org.anchoranalysis.core.system.path.FilePathToUnixStyleConverter: Converts a path to a string using Unix-style separators (forward-slashes)
toStringUnixStyle(Path) - Static method in class org.anchoranalysis.core.system.path.FilePathToUnixStyleConverter: Converts a path to a string using Unix-style separators (forward-slashes)
total() - Method in class org.anchoranalysis.feature.results.ResultsVector
totalAll(MemoCollection, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
TotalCount - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
TotalCount() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.TotalCount
totalIndividual(VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
totalMinusGPUs() - Method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
totalNumber() - Method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
totalNumberSlices() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape: The total number of z-slices across all frames, channels
totalNumberVoxelPositions() - Method in class org.anchoranalysis.spatial.Extent: Calculates the total number of pixel positions needed to represent this bounding box as a pixel array This is not the same as volume, both the start and end pixel are included
ToTextFile - Class in org.anchoranalysis.experiment.bean.log: Logs to a text-file created in the output-directory under a particular name.
ToTextFile() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFile
ToTextFileBase - Class in org.anchoranalysis.experiment.bean.log
ToTextFileBase() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFileBase
ToTextFileOnlyIfFailure - Class in org.anchoranalysis.experiment.bean.log: Logs to a text file like with ToTextFile but the log is ONLY written if a failure occurs in the experiment.
ToTextFileOnlyIfFailure() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFileOnlyIfFailure
ToThePowerOfConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
ToThePowerOfConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
TouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching: Base class for features that calculate touching with a dilated bounding box intersection
TouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
ToUnsignedByte - Class in org.anchoranalysis.image.core.channel.convert: Converts from other data types to UnsignedByteBuffer (unsigned 8-bit) without scaling.
ToUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
ToUnsignedByte() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByte
ToUnsignedByte() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
ToUnsignedByte(VoxelsConverter<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByte
ToUnsignedByteScaleByMinMaxValue - Class in org.anchoranalysis.image.core.channel.convert: Converts from other data types to UnsignedByteBuffer (unsigned 8-bit) scaling from the range of the source data-type.
ToUnsignedByteScaleByMinMaxValue(int, int) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByteScaleByMinMaxValue
ToUnsignedShort - Class in org.anchoranalysis.image.core.channel.convert
ToUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort
ToUnsignedShort() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedShort
ToUnsignedShort(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
ToUnsignedShort(VoxelsConverter<UnsignedShortBuffer>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedShort
toVoxel(int, int, int) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns one particular voxel
toVoxel(Point3i) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns one particular voxel
toVoxels(ImagePlus) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertFromImagePlus: Converts an ImagePlus to a VoxelsWrapper.
transferFrom(int, VoxelBuffer<T>, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
transferFromConvert(int, VoxelBuffer<?>, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
transferSlice(int, VoxelsWrapper, int, boolean) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
transferSlicesResizeXY(VoxelsWrapper, VoxelsWrapper, Interpolator) - Static method in class org.anchoranalysis.image.voxel.interpolator.InterpolateUtilities
transferValue(int, int) - Method in class org.anchoranalysis.math.histogram.Histogram
transform(Collection<File>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
transform(Collection<File>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
transform(Collection<File>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabeticallyWithDirectory
transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Limit
transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RandomOrder
transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching
transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabetically
transform(Optional<W>, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformMapOptional
transform(Assignment) - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary: Transform an existing ColorList.
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Shuffle
transform(VoxelizedMarksWithEnergy, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
transform(ColoredMarksWithDisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
transform(MarkCollection) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
transform(MarkCollection, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
transform(MarkCollection, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.AddEnergy
transform(StateTransformer<T, S>, TransformationContext) - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
transform(DualVoxelizedMarks, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveDestinationFromDual
transform(DualVoxelizedMarks, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveSourceFromDual
transform(MarksFromPartition, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartition
transform(MarksFromPartition, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
transform(ToPixelized<T>, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveDestinationFromVoxelized
transform(ToPixelized<T>, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveSourceFromVoxelized
transform(S, TransformationContext) - Method in class org.anchoranalysis.mpp.segment.transformer.Compose
transform(T) - Method in class org.anchoranalysis.io.generator.OneStageGenerator
transform(T) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
transform(T) - Method in interface org.anchoranalysis.io.generator.TransformingGenerator: Applies any necessary preprocessing to create an element suitable for writing to the filesystem.
transform(T) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
transform(T, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
transform(W, TransformationContext) - Method in interface org.anchoranalysis.mpp.segment.transformer.StateTransformer
TransformationAssignMode<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode: Applies a transformation to the kernel-type U to calculate the Energy used as the primary readout during optimization
TransformationAssignMode() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
TransformationContext - Class in org.anchoranalysis.mpp.segment.transformer
TransformationContext(Dimensions, KernelCalculationContext, Logger) - Constructor for class org.anchoranalysis.mpp.segment.transformer.TransformationContext
TransformingGenerator<T,S> - Interface in org.anchoranalysis.io.generator: Performs preprocessing to transform the element into another type before being written to the filesystem.
TransformingGeneratorBridge<S,T,V> - Class in org.anchoranalysis.io.generator: Allows us to call an SingleFileTypeGenerator<V,S> as if it was an SingleFileTypeGenerator<T,S> using an function to connect the two.
TransformingGeneratorBridge(TransformingGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class org.anchoranalysis.io.generator.TransformingGeneratorBridge
TransformMapOptional<W,X> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
TransformMapOptional(StateTransformer<W, X>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformMapOptional
transpose() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
TraversalResult(List<Path>, List<Path>, int) - Constructor for class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
traverse(Point3i, List<Point3i>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.OutlinePixelsRetriever
traverse(Point3i, List<Point3i>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
TraverseDirectoryForProgressReporter - Class in org.anchoranalysis.core.progress
TraverseDirectoryForProgressReporter.TraversalResult - Class in org.anchoranalysis.core.progress
traverseNotRecursive(Path, Predicate<Path>) - Static method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter
TraverseOutlineException - Exception in org.anchoranalysis.plugin.mpp.bean.outline
TraverseOutlineException(String) - Constructor for exception org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineException
TraverseOutlineException(String, Throwable) - Constructor for exception org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineException
TraverseOutlineOnImage - Class in org.anchoranalysis.plugin.mpp.bean.outline
TraverseOutlineOnImage() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
TraversePointsOnContour - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
TraversePointsOnContour() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
traverseRecursive(Path, int, Predicate<Path>, int) - Static method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter
trigger() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TriggerTerminationCondition
TriggerTerminationCondition - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination
TriggerTerminationCondition() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TriggerTerminationCondition
Tuple3d - Class in org.anchoranalysis.spatial.point
Tuple3d() - Constructor for class org.anchoranalysis.spatial.point.Tuple3d
Tuple3f - Class in org.anchoranalysis.spatial.point
Tuple3f() - Constructor for class org.anchoranalysis.spatial.point.Tuple3f
Tuple3i - Class in org.anchoranalysis.spatial.point
Tuple3i() - Constructor for class org.anchoranalysis.spatial.point.Tuple3i
twoNonOverlappingCircles(boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.FeatureInputOverlappingCircleFixture: Two object-masks of circles in different locations WITHOUT any overlap
twoOverlappingCircles(boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.FeatureInputOverlappingCircleFixture: Two object-masks of circles in different locations WITH some overlap
TwoVoxelMappingBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider: Takes the two channels and creates a NEW third channel whose pixels are a function of the two channels
TwoVoxelMappingBase(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.TwoVoxelMappingBase
TypedEdge<V,P> - Class in org.anchoranalysis.core.graph: An edge that exists in a graph, together with the two vertices that it conntects.
TypedEdge(P, V, V) - Constructor for class org.anchoranalysis.core.graph.TypedEdge
TypedValue - Class in org.anchoranalysis.core.value
TypedValue(double, int) - Constructor for class org.anchoranalysis.core.value.TypedValue
TypedValue(int) - Constructor for class org.anchoranalysis.core.value.TypedValue
TypedValue(String) - Constructor for class org.anchoranalysis.core.value.TypedValue
TypedValue(String, boolean) - Constructor for class org.anchoranalysis.core.value.TypedValue

U

UnaryWithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
UnaryWithChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
UnaryWithMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask
UnaryWithMaskBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
UnaryWithObjectsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider
UnaryWithObjectsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
UnaryWithValueBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider: A ChannelProviderUnary which has a scalar value field
UnaryWithValueBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
UnchangingEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination: TODO consider renaming to ConstantScore
UnchangingEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
UnchangingNumberMarks - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination: TODO consider renaming to constant size
UnchangingNumberMarks() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
unconvertedDataType() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
underlyingBytes() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: An array of bytes that underlies the buffer (and can be written into a file).
UniformProposal<S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme: Repeatedly propose new collections of marks and take the collection with optimal energy.
UniformProposal() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
UniformRandom - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
UniformRandom - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position
UniformRandom() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.UniformRandom
UniformRandom() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
UniformRandomRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.radii
UniformRandomRadiiProposer() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
UniformRandomRadiiProposer(Bound, boolean) - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
union() - Method in class org.anchoranalysis.spatial.box.BoundingBox: For performing a union between this bounding-box and another
uniqueIdentifierFor(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
uniqueIdentifierFor(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
uniqueIdentifierFor(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures: Generates a unique identifier for a particular input
uniqueIdentifierFor(T) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
uniquelyIdentifyAllProperties() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations: A string that uniquely identifies all properties in the bean, but NOT friendly to humans
uniqueName() - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization: A string describing this class and all its parameterization that is guaranteed to be unique for a given set of parameters
uniqueName() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
uniqueName() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
uniqueName() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
unitArea() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
unitConvert() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions: Converts voxelized measurements to/from physical units.
unitConvert() - Method in class org.anchoranalysis.image.core.dimensions.Resolution: Converts voxelized measurements to/from physical units.
UnitConverter - Class in org.anchoranalysis.image.core.dimensions: Converts from voxelized units to different physical measurements of area / volume / distance.
UnitConverter - Class in org.anchoranalysis.plugin.mpp.feature.bean.unit: Converts units (distance, area, volume) to a another representation (e.g.
UnitConverter() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
UnitConverter(Resolution) - Constructor for class org.anchoranalysis.image.core.dimensions.UnitConverter
unitConvertOptional() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
UnitsWithinRange<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.plugin.image.feature.bean.physical: Checks if a value lies within a range defined by units (a minimum and maximum boundary)
UnitsWithinRange() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
UnitTestCompareUtilities - Class in org.anchoranalysis.test.experiment.launcher
UnitValueArea - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
UnitValueArea() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
UnitValueArea(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
UnitValueAreaOrVolume - Class in org.anchoranalysis.image.bean.unitvalue.extent
UnitValueAreaOrVolume() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.UnitValueAreaOrVolume
UnitValueDistance - Class in org.anchoranalysis.image.bean.unitvalue.distance
UnitValueDistance() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
UnitValueException - Exception in org.anchoranalysis.image.bean.nonbean.error
UnitValueException(Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.UnitValueException
UnitValueException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.UnitValueException
UnitValueVolume - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume
UnitValueVolume() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.UnitValueVolume
unitVolume() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
UnsignedBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Base class for buffers that represent an unsigned-type in the signed-equivalent-type NIO Buffer.
UnsignedBuffer(Buffer) - Constructor for class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
UnsignedBufferAsInt - Class in org.anchoranalysis.image.voxel.buffer.primitive: A UnsignedBuffer that exposes its internal types as int.
UnsignedBufferAsInt(Buffer) - Constructor for class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
unsignedByteArray(byte[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an existing array (encoding unsigned bytes as a signed array) as a voxel-buffer.
unsignedByteBuffer(UnsignedByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-byte buffer into a voxel-buffer.
UnsignedByteBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Wraps a ByteBuffer but automatically performs conversion to int.
UnsignedByteFromFloat - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
UnsignedByteFromFloat(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
UnsignedByteFromUnsignedByteInterleaving - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
UnsignedByteFromUnsignedByteInterleaving() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
UnsignedByteFromUnsignedByteNoInterleaving - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
UnsignedByteFromUnsignedByteNoInterleaving() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
UnsignedByteFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
UnsignedByteFromUnsignedInt(int, boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
UnsignedByteFromUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
UnsignedByteFromUnsignedShort(boolean, int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
unsignedByteRaw(ByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-byte buffer (represented by a NIO signed-buffer) into a voxel-buffer.
unsignedByteToInt(byte) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
unsignedByteToShort(byte) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
UnsignedByteVoxelType - Class in org.anchoranalysis.image.voxel.datatype
unsignedIntArray(int[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-int buffer into a voxel-buffer.
unsignedIntBuffer(UnsignedIntBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-int buffer (represented by a NIO signed-buffer) into a voxel-buffer.
UnsignedIntBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Wraps an IntBuffer but automatically performs conversion to long.
UnsignedIntFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.toint
UnsignedIntFromUnsignedInt(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
unsignedIntToInt(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
unsignedIntToLong(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
unsignedIntToShort(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
UnsignedIntVoxelType - Class in org.anchoranalysis.image.voxel.datatype
unsignedShortArray(short[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an existing array (encoding unsigned shorts as a signed array) as a voxel-buffer.
unsignedShortBuffer(UnsignedShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-short buffer into a voxel-buffer.
UnsignedShortBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Wraps a ShortBuffer but automatically performs conversion to int.
UnsignedShortFromSignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort
UnsignedShortFromSignedShort(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromSignedShort
UnsignedShortFromUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort
UnsignedShortFromUnsignedShort(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromUnsignedShort
unsignedShortRaw(ShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-short buffer (represented by a NIO signed-buffer) into a voxel-buffer.
unsignedShortToInt(short) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
UnsignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype
UnsignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype
UnsignedVoxelType(int, String, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
UnsupportedMarkTypeException - Exception in org.anchoranalysis.mpp.mark
UnsupportedMarkTypeException(Exception) - Constructor for exception org.anchoranalysis.mpp.mark.UnsupportedMarkTypeException
UnsupportedMarkTypeException(String) - Constructor for exception org.anchoranalysis.mpp.mark.UnsupportedMarkTypeException
untilFirstIntensityEqualTo(BoundedVoxels<UnsignedByteBuffer>, byte) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: Iterates each voxel until a specific intensity value is found.
UpdatableBeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition: Rather than checking if obj1 vs obj2 is accepted instead there's a two stage process
UpdatableMarkSet - Interface in org.anchoranalysis.mpp.mark.set
UpdatablePointsContainer - Class in org.anchoranalysis.mpp.bean.points.updatable
UpdatablePointsContainer() - Constructor for class org.anchoranalysis.mpp.bean.points.updatable.UpdatablePointsContainer
update() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
update(double) - Method in class org.anchoranalysis.core.progress.ProgressReporterMultiple
update(int) - Method in interface org.anchoranalysis.core.progress.ProgressReporter
update(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
update(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
update(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
update(Integer) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
update(Integer) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
update(String) - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
update(Point2d, Point2d, Orientation2D) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
update(T) - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelDeathPixelized
updateAfterAcceptance(ListUpdatableMarkSetCollection, MarkCollection, MarkCollection) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
updateAfterAcceptance(ListUpdatableMarkSetCollection, MarksFromPartition, MarksFromPartition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
updateAfterAcceptance(ListUpdatableMarkSetCollection, MarksFromPartition, MarksFromPartition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelDeathPartition
updateAfterAcceptance(ListUpdatableMarkSetCollection, MarksFromPartition, MarksFromPartition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
updateAfterAcceptance(ListUpdatableMarkSetCollection, T, T) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel: If the kernel is accepted, makes the necessary changes to a ListUpdatableMarkSetCollection
updateAfterAcceptance(ListUpdatableMarkSetCollection, T, T) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
updateAfterMarkChange() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.PointList
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
updateIndex(String, int) - Method in class org.anchoranalysis.io.generator.sequence.SequenceMemory
updateLabeling(double) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm: Update labels with the specified slack by adding the slack value for committed workers and by subtracting the slack value for committed jobs.
UpdateMarkSetException - Exception in org.anchoranalysis.mpp.mark.set
UpdateMarkSetException(Exception) - Constructor for exception org.anchoranalysis.mpp.mark.set.UpdateMarkSetException
UpdateMarkSetException(String) - Constructor for exception org.anchoranalysis.mpp.mark.set.UpdateMarkSetException
updateResolution(Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.Channel
updateResolution(Resolution) - Method in class org.anchoranalysis.image.core.stack.Stack
updateShellRad(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
updateSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.UpdatableBeforeCondition
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
updateTotal(MemoCollection, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
UpperLowerQuantileIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel
UpperLowerQuantileIntensity(double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.UpperLowerQuantileIntensity
UpperLowerQuantileIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram: Scales by a lower and upper quantile of the intensity values of an image
UpperLowerQuantileIntensityFromHistogram(double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
UpperLowerQuantileIntensityFromHistogram(double, double, double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
useDefault() - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Use default manager.
UseDefaultManager - Class in org.anchoranalysis.launcher.executor.selectparam: Uses whatever default-manager exists
UseDefaultManager() - Constructor for class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.Experiment: Whether to detail more (a lengthy experiment) or less (something quick and simple - suitable for console)?
useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
useDetailedLogging() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
useDetailedLogging() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
useDetailedLogging() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
useDetailedLogging() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold: Uses calculateLevelElse instead of the standard calculation-level approach
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
useZ - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent

V

valueByDimension(int) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
valueByDimension(int) - Method in class org.anchoranalysis.spatial.Extent
valueByDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
valueByDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3f
valueByDimension(AxisType) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
valueByDimension(AxisType) - Method in class org.anchoranalysis.spatial.Extent
valueByDimension(AxisType) - Method in class org.anchoranalysis.spatial.point.Tuple3d
valueByDimension(AxisType) - Method in class org.anchoranalysis.spatial.point.Tuple3f
valueFor(SessionInput<FeatureInputSingleObject>, ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
valueFor(SessionInput<FeatureInputSingleObject>, ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
valueFor(SessionInput<FeatureInputSingleObject>, ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjects
valueFor(AxisType, int, int, int) - Static method in class org.anchoranalysis.spatial.axis.AxisTypeConverter: Multiplexes the correct value for the given dimension
valueFromFirst(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
valueFromMerged(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
valueFromSecond(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
valueOf(String) - Static method in enum org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.anchoranalysis.image.core.channel.convert.ConversionPolicy: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.anchoranalysis.image.voxel.object.morphological.SelectDimensions: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.anchoranalysis.spatial.axis.AxisType: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.anchoranalysis.image.core.channel.convert.ConversionPolicy: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.anchoranalysis.image.voxel.object.morphological.SelectDimensions: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.anchoranalysis.spatial.axis.AxisType: Returns an array containing the constants of this enum type, in the order they are declared.
variance() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
variance() - Method in class org.anchoranalysis.math.histogram.Histogram
variance() - Method in class org.anchoranalysis.math.statistics.VarianceCalculator: Calculate the variance
Variance - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Variance() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Variance
VarianceCalculator - Class in org.anchoranalysis.math.statistics: Helper class for calculating variance from running variables
VarianceCalculator() - Constructor for class org.anchoranalysis.math.statistics.VarianceCalculator
VarianceCalculator(long, long, long) - Constructor for class org.anchoranalysis.math.statistics.VarianceCalculator
VarianceFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
VarianceFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.VarianceFilter2D
Vector3d - Class in org.anchoranalysis.spatial.point
Vector3d() - Constructor for class org.anchoranalysis.spatial.point.Vector3d
Vector3d(double, double, double) - Constructor for class org.anchoranalysis.spatial.point.Vector3d
Vector3d(Tuple3d) - Constructor for class org.anchoranalysis.spatial.point.Vector3d
VectorInDirection - Class in org.anchoranalysis.image.bean.spatial.direction
VectorInDirection() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
VectorInDirection(double, double, double) - Constructor for class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
VectorInDirection(DirectionVector) - Constructor for class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
verifySeedsAreInside(Extent) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
vertices() - Method in class org.anchoranalysis.core.graph.GraphWithPayload: The set of all vertices in the graph.
verticesAsObjects() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
VeryBright - Class in org.anchoranalysis.bean.shared.color.scheme: Creates a list by repeating a defined list of very bright colors.
VeryBright() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.VeryBright
VisitedVoxels - Class in org.anchoranalysis.image.core.outline.traverser.visited: All pixels that have been visited so far
VisitedVoxels() - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
VisitScheduler - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
VisitScheduler() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
VisitSchedulerAnd - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
VisitSchedulerAnd() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
VisitSchedulerConvexAboutRoot - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
VisitSchedulerConvexAboutRoot() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
VisitSchedulerMaxDistanceAlongContour - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
VisitSchedulerMaxDistanceAlongContour() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
VisitSchedulerUniformSample - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
VisitSchedulerUniformSample() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
visualization() - Method in interface org.anchoranalysis.mpp.probmap.ProbMap
visualization() - Method in class org.anchoranalysis.mpp.probmap.ProbMapObjects
VisualizeOnBackground - Class in org.anchoranalysis.plugin.mpp.bean.define: Adds a visualization for all binary-masks and object-collections that are added using a particular background
VisualizeOnBackground() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Circle
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
volume(int) - Method in class org.anchoranalysis.mpp.mark.Mark
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.PointList
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
Volume<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: Calculates the volume (x, y and z dimensions) of the scene from the dimensions
Volume - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
Volume() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Volume
Volume() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.Volume
volumeAgg(VoxelizedMarkMemo, VoxelizedMarkMemo, int, RelationBean, LongBinaryOperator) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
VolumeMin - Class in org.anchoranalysis.plugin.mpp.bean.check
VolumeMin() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
VolumePhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume
VolumePhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
volumeStatistic(VoxelizedMarkMemo, VoxelizedMarkMemo, int, RelationBean, LongBinaryOperator) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
VolumeVoxels - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume
VolumeVoxels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
VolumeVoxels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
volumeXY() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
volumeXY() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer: How many pixels in an XY slice
volumeXY() - Method in class org.anchoranalysis.spatial.Extent
voxel(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.extracter.Base
voxel(ReadableTuple3i) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Gets the value of one particular value
voxelAtBufferIndex(T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
VoxelBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer: A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
VoxelBuffer() - Constructor for class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
VoxelBufferFactory - Class in org.anchoranalysis.image.voxel.buffer: Creating voxel-buffers and arrays of voxel-buffers of various types.
VoxelBufferWrap - Class in org.anchoranalysis.image.voxel.buffer: Wraps arrays and buffers of primitive-types into VoxelBuffer.
VoxelDataType - Class in org.anchoranalysis.image.voxel.datatype: The type of data one voxel represents in an image-channel.
VoxelDataType(int, String, long, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.VoxelDataType
VoxelDataTypeFactoryMultiplexer<T> - Class in org.anchoranalysis.image.voxel.datatype: Multiplexes between factories for the various VoxelDataTypes.
VoxelDataTypeFactoryMultiplexer(T, T, T, T) - Constructor for class org.anchoranalysis.image.voxel.datatype.VoxelDataTypeFactoryMultiplexer
voxelized() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: A voxelized-respentation of the mark
VoxelizedMark - Interface in org.anchoranalysis.mpp.mark.voxelized: A voxelized representation of a Mark i.e.
VoxelizedMarkFactory - Class in org.anchoranalysis.mpp.mark.voxelized
VoxelizedMarkMemo - Class in org.anchoranalysis.mpp.mark.voxelized.memo: Memoization of retrieving a VoxelizedMark from a mark
VoxelizedMarkMemo(Mark, EnergyStackWithoutParams, RegionMap) - Constructor for class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
VoxelizedMarksChangeReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
VoxelizedMarksChangeReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
VoxelizedMarksPeriodicReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
VoxelizedMarksPeriodicReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
VoxelizedMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy.marks: A collection of marks, their voxelized equivalents, and associated energy.
VoxelizedMarksWithEnergy(MarksWithEnergyBreakdown, EnergyStack, SharedFeatureMulti, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
VoxelizedMarksWithEnergyFactory - Class in org.anchoranalysis.plugin.mpp.segment.optimization
VoxelizeWithTransform<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized: Converts a Marks to a MarksToPixelized using a transformer
VoxelizeWithTransform() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
VoxelizeWithTransform(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
VoxelPartition<T> - Interface in org.anchoranalysis.mpp.voxel.partition: A partition of voxels
VoxelPartitionFactory<T> - Interface in org.anchoranalysis.mpp.voxel.partition.factory
VoxelPartitionFactoryHistogramReuse - Class in org.anchoranalysis.mpp.voxel.partition.factory
VoxelPartitionFactoryHistogramReuse() - Constructor for class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactoryHistogramReuse
VoxelPartitionHistogram - Class in org.anchoranalysis.mpp.voxel.partition
VoxelPartitionHistogram(int, Supplier<Histogram>) - Constructor for class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
VoxelPartitonFactoryHistogram - Class in org.anchoranalysis.mpp.voxel.partition.factory
VoxelPartitonFactoryHistogram() - Constructor for class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitonFactoryHistogram
VoxelPhysicalSize<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions: The physical size of a pixel in a specific dimension.
VoxelPhysicalSize() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize
voxels - Variable in class org.anchoranalysis.image.voxel.extracter.Base: The voxels to extract from
voxels() - Method in class org.anchoranalysis.image.core.channel.Channel
voxels() - Method in class org.anchoranalysis.image.core.mask.Mask
voxels() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Voxels that should only have two intensity-values (representing ON and OFF states).
voxels() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Voxel-data that fits inside the bounding-box (its extent is invariant with the extent of the bounding-box).
voxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
voxels() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
voxels() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
Voxels<T> - Class in org.anchoranalysis.image.voxel: A box (3-dimensions) with voxel-data.
Voxels(SliceBufferIndex<T>, VoxelsFactoryTypeBound<T>, VoxelsArithmetic) - Constructor for class org.anchoranalysis.image.voxel.Voxels
VoxelsArithmetic - Interface in org.anchoranalysis.image.voxel.arithmetic
VoxelsArithmeticFactory - Class in org.anchoranalysis.image.voxel.arithmetic
VoxelsAsFloat - Class in org.anchoranalysis.image.voxel
VoxelsAsFloat(SliceBufferIndex<FloatBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsAsFloat
VoxelsAsInt - Class in org.anchoranalysis.image.voxel
VoxelsAsInt(SliceBufferIndex<UnsignedIntBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsAsInt
VoxelsAsShort - Class in org.anchoranalysis.image.voxel
VoxelsAsShort(SliceBufferIndex<UnsignedShortBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsAsShort
VoxelsAssigner - Interface in org.anchoranalysis.image.voxel.assigner: Assigns values to some or all voxels
VoxelsAssignerFactory - Class in org.anchoranalysis.image.voxel.assigner
VoxelsConverter<T> - Class in org.anchoranalysis.image.voxel.convert: Converts voxels from one data-type to another.
VoxelsConverter() - Constructor for class org.anchoranalysis.image.voxel.convert.VoxelsConverter
VoxelScore - Class in org.anchoranalysis.image.feature.bean.score: Calculates a per-voxel score
VoxelScore() - Constructor for class org.anchoranalysis.image.feature.bean.score.VoxelScore
voxelsEqualTo(int) - Method in class org.anchoranalysis.image.core.channel.Channel: Operations on whether particular voxels are equal to a particular value
voxelsEqualTo(int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
voxelsEqualTo(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Operations on whether particular voxels are equal to a particular value
VoxelsExtracter<T> - Interface in org.anchoranalysis.image.voxel.extracter: Provides method to read/copy/duplicate portions of voxels
VoxelsExtracterFactory - Class in org.anchoranalysis.image.voxel.extracter
VoxelsFactory - Class in org.anchoranalysis.image.voxel.factory
VoxelsFactoryTypeBound<T> - Interface in org.anchoranalysis.image.voxel.factory: A factory for creating voxels with a particular buffer-type
voxelsGreaterThan(int) - Method in class org.anchoranalysis.image.core.channel.Channel: Operations on whether particular voxels are greater than a treshold (but not equal to)
voxelsGreaterThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
voxelsGreaterThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Operations on whether particular voxels are greater than a treshold (but not equal to)
voxelsMaximumIntensityProjection() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
voxelsOff() - Method in class org.anchoranalysis.image.core.mask.Mask
voxelsOff() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
voxelsOn() - Method in class org.anchoranalysis.image.core.mask.Mask
voxelsOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
VoxelsPredicate - Interface in org.anchoranalysis.image.voxel.extracter.predicate: Methods to find or count voxels that satisfy a predicate.
VoxelStatistics - Interface in org.anchoranalysis.image.voxel.statistics: Allows retrieval of statistics about voxel intensities.
VoxelStatisticsCombined - Class in org.anchoranalysis.image.voxel.statistics
VoxelStatisticsCombined() - Constructor for class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
VoxelStatisticsFromHistogram - Class in org.anchoranalysis.image.voxel.statistics
VoxelStatisticsFromHistogram(Histogram) - Constructor for class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
VoxelsThresholder - Class in org.anchoranalysis.image.voxel.thresholder: Performs threshold operation on voxels.
VoxelsUnsignedByte - Class in org.anchoranalysis.image.voxel
VoxelsUnsignedByte(SliceBufferIndex<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
VoxelsWrapper - Class in org.anchoranalysis.image.voxel: Wraps a voxels associated with a channel so it can be easily casted to an appropriate data type
VoxelsWrapper(Voxels<?>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsWrapper
VoxelsWrapperList - Class in org.anchoranalysis.image.voxel
VoxelsWrapperList() - Constructor for class org.anchoranalysis.image.voxel.VoxelsWrapperList
voxelWithMaxIntensity() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Finds the maximum-value of any voxel and rounds up (ceiling) to nearest long

W

WatershedEncoding - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
WatershedEncoding() - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
WatershedYeong - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong: A 'rainfall' watershed algorithm
WatershedYeong() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
WeightedKernel<T> - Class in org.anchoranalysis.mpp.segment.kernel.proposer: A kernel with an associated weight.
WeightedKernel(Kernel<T>, double) - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel: Constructor for single kernel factory
WeightedKernelList<T> - Class in org.anchoranalysis.mpp.segment.kernel.proposer
WeightedKernelList() - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
weightFor(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ConstantWeight
weightFor(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ExtractWeightFromMark
weightFor(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.NumberPoints
weightWidthDescription() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
weightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
weightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
WholeImageLabelAnnotationReader - Class in org.anchoranalysis.annotation.io.image
WholeImageLabelAnnotationReader() - Constructor for class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationReader
WholeImageLabelAnnotationWriter - Class in org.anchoranalysis.annotation.io.image
WholeImageLabelAnnotationWriter() - Constructor for class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationWriter
WholeImageLabelStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
WholeImageLabelStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
with(Feature<T>, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession: Starts a feature-session for a single feature
with(Feature<T>, FeatureInitParams, SharedFeatureMulti, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
with(Feature<T>, SharedFeatureMulti, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession: Starts a feature-session for a single feature
with(FeatureList<T>, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession: Starts a feature-session for a list of features
with(FeatureList<T>, FeatureInitParams, Optional<SharedFeatureMulti>, Logger, BoundReplaceStrategy<T, ? extends ReplaceStrategy<T>>) - Static method in class org.anchoranalysis.feature.session.FeatureSession
with(FeatureList<T>, FeatureInitParams, SharedFeatureMulti, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
with(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection
with(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxUnion: Performs a union with another box (immutably)
withBuffer(Optional<ObjectMask>, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional: Iterate over each voxel on an object-mask with one associated buffer.
withBuffer(Mask, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.core.mask.IterateVoxelsMask: Iterate over each voxel in a mask - with an associated buffer for each slice from a voxel-bo
withBuffer(ObjectMask, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel in an object-mask - with one associated buffer for each slice from Voxels.
withBuffer(Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with one associated buffer for each slice.
withBuffer(BoundingBox, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with one associated buffer for each slice
withCalculateLevel(Histogram, CalculateLevel) - Static method in class org.anchoranalysis.plugin.image.intensity.HistogramThresholder: Retains the portion of the histogram greater or equal to the calculated-level
WithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
WithChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
WithConfidence<T> - Class in org.anchoranalysis.plugin.image.segment: Wraps an element with a confidence-score and imposes an ordering (highest confidence first).
WithConfidence(T, double) - Constructor for class org.anchoranalysis.plugin.image.segment.WithConfidence
WithContainerBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProvider that take an optional objectsContainer bean-field.
WithContainerBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
WithDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviderUnary classes that require dimensions to be specified.
WithDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
within(Optional<ObjectMask>, Extent, ProcessVoxelNeighborAbsolute<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory: Within either an object-mask or an extent (as a fallback)
withinExtent(ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory
withinMask(ObjectMask, ProcessChangedPointAbsoluteMasked<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory
withinMask(ObjectMask, ProcessVoxelNeighborAbsolute<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory
withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase: What value to return if the value is inside the range
withInside(BoundingBox, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection: Find the intersection and clip to a a containing extent
withLabel(String) - Method in class org.anchoranalysis.experiment.log.Divider: Creates a line of repeated dashes with a centered label of text.
withMatchingPoints(BoundingBox, Predicate<Point3i>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box that matches a predicate.
WithOptionalDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider: Base class for ObjectCollectionProviderUnary classes that offer an optional means to specify dimensions.
WithOptionalDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
withoutColor() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
withoutLabel() - Method in class org.anchoranalysis.experiment.log.Divider: Creates a line of repeated dashes.
withoutOrder(OutputPatternStringSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Writes elements (indexed by strings) to directory, without any order in the sequence.
withoutOrderCurrentDirectory(String) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory: Writes elements (indexed by strings) to the current directory, without any order in the sequence.
withoutParams() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The energy-stack without associated parameters.
withoutProgressReporter() - Method in interface org.anchoranalysis.core.progress.CheckedProgressingSupplier
withoutProperties() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties: Returns the contained-objects without corresponding properties
withoutProperties() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
withoutUniformSizeConstraint() - Method in class org.anchoranalysis.image.core.stack.NamedStacksUniformSize
withPoint(Optional<ObjectMask>, Extent, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional: Iterate over all points that are located on a object-mask or else all points in an extent.
withPoint(ObjectMask, Optional<ObjectMask>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each point that is located on an object-mask AND optionally a second-mask
withPoint(ObjectMask, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel that is located on an object-mask
withPoint(BoundingBox, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box
withPoint(Extent, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in an Extent
WithPriority<T> - Class in org.anchoranalysis.core.concurrency
WithPriority(T, boolean) - Constructor for class org.anchoranalysis.core.concurrency.WithPriority
WithRadiusBase - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider: A ChannelProviderUnary with a 'radius' parameter
WithRadiusBase() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
WithResolutionBase<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
WithResolutionBase() - Constructor for class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
WithResolutionBase(Feature<T>) - Constructor for class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
withSlidingBuffer(Optional<ObjectMask>, SlidingBuffer<?>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional: Iterate over each voxel in a sliding-buffer, optionally restricting it to be only voxels in a certain object
withThreeBuffers(Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with three associated buffers for each slice.
withThreeBuffers(BoundingBox, ReadableTuple3i, ReadableTuple3i, Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with three associated buffers for each slice.
withTwoBuffers(BoundedVoxels<T>, BoundedVoxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded: Iterates over the intersection of two bounded-voxels of type BoundedVoxels.
withTwoBuffers(ObjectMask, Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel with a corresponding ON value in an object-mask - and with two associated buffers for each slice covering the all the global space i.e.
withTwoBuffers(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, ProcessBufferBinary<UnsignedByteBuffer, UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded: Iterates over the intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask.
withTwoBuffers(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with two associated buffers for each slice, one VoxelBuffer and one Buffer
withTwoBuffersAndPoint(Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with two associated buffers for each slice
withTwoBuffersUntil(BoundedVoxels<T>, BoundedVoxels<T>, PredicateBufferBinary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded: Iterates over the intersection of two bounded-voxels of type BoundedVoxels until a predicate is satisfied.
withTwoBuffersUntil(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, PredicateBufferBinary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with two associated buffers for each slice - until a predicate evaluates to true.
withTwoBuffersWithoutOffset(VoxelBuffer<S>, VoxelBuffer<T>, ProcessBufferBinaryWithoutOffset<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsRemaining: Iterate over remaining voxels each voxel - with two associated buffers for each slice.
withTwoMixedBuffers(BoundingBox, ReadableTuple3i, Voxels<S>, Voxels<T>, ProcessBufferBinaryMixed<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with two associated buffers for each slice.
withTwoVoxelBuffers(Voxels<S>, Voxels<T>, ProcessVoxelBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in a bounding-box - with two associated voxel-buffers for each slice
WithValueBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean: Operations that use a specified constant value
WithValueBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
withVoxelBuffer(ObjectMask, Voxels<T>, Optional<BoundingBox>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel on an object-mask with one associated VoxelBuffer.
withVoxelBuffer(ObjectMask, Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel on an object-mask with one associated VoxelBuffer.
withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with one associated voxel-buffer for each slice.
withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnaryWithPoint<T, E>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with one associated voxel-buffer for each slice.
wrap(String, Throwable) - Static method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
wrap(Voxels<?>) - Static method in class org.anchoranalysis.image.voxel.VoxelsWrapper
Wrap - Class in org.anchoranalysis.image.voxel.convert.imglib2
WrapAbsoluteAsMasked<T> - Class in org.anchoranalysis.image.voxel.iterator.neighbor: Wraps a ProcessVoxelNeighborAbsolute as a ProcessChangedPointAbsoluteMasked
WrapAbsoluteAsMasked(ProcessVoxelNeighborAbsolute<T>) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
WrapAsUpdatable - Class in org.anchoranalysis.plugin.image.object.merge.condition: Wraps a BeforeCondition as an UpdatableBefoerCondition
WrapAsUpdatable(BeforeCondition) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
wrapDuplicate(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Wraps an existing list, WITHOUT reusing the list in the internals of the FeatureList i.e.
wrapRaw(byte[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Exposes a raw byte-array as a buffer with unsigned-bytes.
wrapRaw(int[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Exposes a raw int-array as a buffer with unsigned-ints.
wrapRaw(short[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Exposes a raw short-array as a buffer with unsigned-shorts.
wrapRaw(ByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Exposes a raw ByteBuffer as a buffer with unsigned-bytes.
wrapRaw(IntBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Exposes a raw UnsignedIntBuffer as a buffer with unsigned-ints.
wrapRaw(ShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Exposes a raw UnsignedShortBuffer as a buffer with unsigned-shorts.
wrapReuse(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Wraps an existing list, reusing the list in the internals of the FeatureList
WrapStackAsTimeSequence - Class in org.anchoranalysis.image.core.stack.wrap
WrapStackAsTimeSequence(NamedProvider<Stack>) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequence
WrapStackAsTimeSequenceStore - Class in org.anchoranalysis.image.core.stack.wrap
WrapStackAsTimeSequenceStore(NamedProviderStore<Stack>) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
WrapStackAsTimeSequenceStore(NamedProviderStore<Stack>, int) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
WrapTimeSequenceAsStack - Class in org.anchoranalysis.image.core.stack.wrap
WrapTimeSequenceAsStack(NamedProvider<TimeSequence>) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapTimeSequenceAsStack
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in interface org.anchoranalysis.io.output.writer.Writer: Writes an element using an ElementWriter to the current directory.
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: Writes an element using an ElementWriter to the current directory.
write(Collection<T>, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.collection.CollectionGenerator
write(ImageLabelAnnotation, Path) - Method in class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationWriter
write(DualMarksAnnotation<T>, Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
write(ObjectCollectionWithProperties, RGBStack, ObjectDrawAttributes) - Method in class org.anchoranalysis.overlay.bean.DrawObject
write(ObjectCollectionWithProperties, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class org.anchoranalysis.overlay.bean.DrawObject
write(Manifest, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.ManifestGenerator
write(S, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.GeneratorBridge
write(T, Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationWriter: Saves the annotation to the filesystem
write(T, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.CombinedListGenerator
write(T, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
write(T, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
write(T, OutputNameStyle, OutputterChecked) - Method in interface org.anchoranalysis.io.output.writer.ElementWriter: Writes a non-indexable output (an output that isn't part of a collection of other similar items)
writeEnergyStack() - Method in class org.anchoranalysis.mpp.io.output.EnergyStackWriter
writeFeaturesToCSV(CSVWriter, List<ImageAnnotation>, List<String>) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AnnotationAggregateCSVGenerator
writeFeaturesToCSV(CSVWriter, ResultsVectorList, List<String>) - Method in class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorHorizontal
writeFeaturesToCSV(CSVWriter, ResultsVectorList, List<String>) - Method in class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorVertical
writeFeaturesToCSV(CSVWriter, T, List<String>) - Method in class org.anchoranalysis.feature.io.csv.FeatureTableCSVGenerator: Writes the features to the CSV-file.
writeFileToOperationRecorder(String, Path, ManifestDescription, String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked: Writes a file-entry to the operation recorder
writeGroupedResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures: Writes all the results that have been collected as a CSV file.
writeGroupOutputInSubdirectory(String, T, ConsistentChannelChecker, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
writeGroupResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, InputOutputContext, InputOutputContextSubdirectoryCache) - Method in class org.anchoranalysis.feature.io.results.group.GroupWriter: Writes outputs for groups that have been previously added with GroupWriter.addResultsFor(org.anchoranalysis.feature.io.csv.RowLabels, org.anchoranalysis.feature.results.ResultsVector).
writeHeaders(List<String>) - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase: Creates a channel with the levels for a set of objects
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
writeOffByte(int, UnsignedByteBuffer) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
WriteOperationRecorder - Interface in org.anchoranalysis.io.manifest.operationrecorder: Makes a record of an output written to the filesystem.
writeOverlays(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>) - Method in class org.anchoranalysis.overlay.writer.DrawOverlay: Writes a collection of colored-overlays to the background
writeOverlaysIfIntersects(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>, List<BoundingBox>) - Method in class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
writeOverlaysIfIntersects(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>, List<BoundingBox>) - Method in class org.anchoranalysis.overlay.writer.DrawOverlay
writePrecalculatedMask(RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.overlay.writer.PrecalculationOverlay
writePrecalculatedOverlays(List<PrecalculationOverlay>, Dimensions, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
writePrecalculatedOverlays(List<PrecalculationOverlay>, Dimensions, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class org.anchoranalysis.overlay.writer.DrawOverlay
Writer - Interface in org.anchoranalysis.io.output.writer: Write data via ElementWriters to the file system, or creates new sub-directories for writing data to.
writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter: Writes an annotation to the filesystem at outPath.
writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
writeResolutionXml(Resolution, Path) - Static method in class org.anchoranalysis.plugin.io.xml.ResolutionAsXml: Writes a XML metadata file describing the image-resolution.
WriteResolutionXml - Class in org.anchoranalysis.plugin.io.bean.stack.writer: When writing a stack, an additional file is written to indicate the physical voxel sizes, if this information is known.
WriteResolutionXml() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
writeResultsForAllGroups(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, InputOutputContext) - Method in class org.anchoranalysis.feature.io.results.ResultsWriter: Writes the stored-results to CSV files.
WriterExecuteBeforeEveryOperation - Interface in org.anchoranalysis.io.output.writer
writeRGBColorToByteArray(RGBColor, Point3i, Dimensions, UnsignedByteBuffer, UnsignedByteBuffer, UnsignedByteBuffer) - Static method in class org.anchoranalysis.image.core.stack.rgb.RGBOutputUtils
writeRGBMaskToSlice(ObjectMask, BoundingBox, RGBColor, Point3i, int, ReadableTuple3i) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
writeRGBPoint(Point3i, RGBColor) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
writerMultiplex(boolean) - Method in class org.anchoranalysis.io.output.outputter.Outputter: Multiplexes between the selective and permissive writers based on a flag.
writeRow(String, int, double) - Method in class org.anchoranalysis.plugin.image.task.slice.SharedStateSelectedSlice
writeRow(String, String) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
writeRow(List<TypedValue>) - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
writerPermissive() - Method in class org.anchoranalysis.io.output.outputter.Outputter: The writer that allows all outputs.
WriterRouterErrors - Class in org.anchoranalysis.io.output.writer: Write data via ElementWriters to the file system, or creates new sub-directories for writng data to.
WriterRouterErrors(Writer, ErrorReporter) - Constructor for class org.anchoranalysis.io.output.writer.WriterRouterErrors
writers() - Method in interface org.anchoranalysis.io.generator.sequence.OutputSequence
writers() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing
writers() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed
writerSecondLevel(String) - Method in class org.anchoranalysis.io.output.outputter.Outputter: A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.
writerSelective() - Method in class org.anchoranalysis.io.output.outputter.Outputter: The writer that allows only certain selected outputs.
WriterUtilities - Class in org.anchoranalysis.annotation.io
writeSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.overlay.bean.DrawObject: Draws a single-object on top of a RGB-stack
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
writeStackAfterCheck(Stack, Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.ImageIOWriter
writeStackAfterCheck(Stack, Path) - Method in class org.anchoranalysis.plugin.opencv.bean.writer.OpenCVWriter
writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.NoTimeSeries
writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.SupportsTimeSeries
writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter
writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
writeStackTime(Stack, Path, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter: Writes a stack as a time-sequence (many images together in a single file.).
WriteStringToFile - Class in org.anchoranalysis.io.generator.text
writeThresholdedByte(int, UnsignedByteBuffer, VoxelBuffer<?>, VoxelBuffer<?>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
writeToFile(String, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.text.StringGenerator
writeToFile(Path) - Method in class org.anchoranalysis.core.value.KeyValueParams: Serializes the key-value params to a file
writeToFile(KeyValueParams, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.feature.io.csv.FeatureTableCSVGenerator
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.XStreamGenerator
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
writeToXML(CSVRow, Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
writeToXML(CSVRow, Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
writeToXML(CSVRow, Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
writeToXML(Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
writeWithIndex(Collection<T>, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.collection.CollectionGenerator
writeWithIndex(Manifest, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.ManifestGenerator
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in interface org.anchoranalysis.io.output.writer.Writer: Writes an indexed-element using an ElementWriter in the current directory.
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors: Writes an indexed-element using an ElementWriter in the current directory.
writeWithIndex(S, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.GeneratorBridge
writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.CombinedListGenerator
writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in interface org.anchoranalysis.io.output.writer.ElementWriter: Writes an indexable output (many outputs of the same type, uniquely identified by an index)
writeXmlToFile(Document, Path) - Static method in class org.anchoranalysis.io.output.xml.XMLWriter: Writes a XML-document to the file-system.

X

x - Variable in class org.anchoranalysis.spatial.point.Tuple3d
x - Variable in class org.anchoranalysis.spatial.point.Tuple3f
x - Variable in class org.anchoranalysis.spatial.point.Tuple3i
x() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
x() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
x() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
x() - Method in class org.anchoranalysis.spatial.Extent
x() - Method in class org.anchoranalysis.spatial.point.Point2d
x() - Method in class org.anchoranalysis.spatial.point.Point2f
x() - Method in class org.anchoranalysis.spatial.point.Point2i
x() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
x() - Method in class org.anchoranalysis.spatial.point.Tuple3d
x() - Method in class org.anchoranalysis.spatial.point.Tuple3f
x() - Method in class org.anchoranalysis.spatial.point.Tuple3i
x() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
x(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
x(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Is this value in the x-dimension within the bounding box range?
X - org.anchoranalysis.spatial.axis.AxisType
X_Y_ONLY - org.anchoranalysis.image.voxel.object.morphological.SelectDimensions: The dilation applies in X and Y -dimensions only, and not in Z-dimension.
xFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
XMLGenerator<T> - Class in org.anchoranalysis.io.generator.xml
XMLGenerator() - Constructor for class org.anchoranalysis.io.generator.xml.XMLGenerator
XmlUtilities - Class in org.anchoranalysis.bean.xml
XMLWriter - Class in org.anchoranalysis.io.output.xml
Xor - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result.
Xor() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Xor
XStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize: Deserializes an object using the XStream library.
XStreamDeserializer() - Constructor for class org.anchoranalysis.core.serialize.XStreamDeserializer
XStreamGenerator<T> - Class in org.anchoranalysis.io.generator.serialized
XStreamGenerator() - Constructor for class org.anchoranalysis.io.generator.serialized.XStreamGenerator
XStreamGenerator(Optional<String>) - Constructor for class org.anchoranalysis.io.generator.serialized.XStreamGenerator
XStreamSerializer - Class in org.anchoranalysis.core.serialize: Serializes an object using the XStream library.
XYOrientationExtendToZ - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points
XYOrientationExtendToZ() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ

Y

y - Variable in class org.anchoranalysis.spatial.point.Tuple3d
y - Variable in class org.anchoranalysis.spatial.point.Tuple3f
y - Variable in class org.anchoranalysis.spatial.point.Tuple3i
y() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
y() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
y() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
y() - Method in class org.anchoranalysis.spatial.Extent
y() - Method in class org.anchoranalysis.spatial.point.Point2d
y() - Method in class org.anchoranalysis.spatial.point.Point2f
y() - Method in class org.anchoranalysis.spatial.point.Point2i
y() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
y() - Method in class org.anchoranalysis.spatial.point.Tuple3d
y() - Method in class org.anchoranalysis.spatial.point.Tuple3f
y() - Method in class org.anchoranalysis.spatial.point.Tuple3i
y() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
y(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
y(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Is this value in the y-dimension within the bounding box range?
Y - org.anchoranalysis.spatial.axis.AxisType
yFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection

Z

z - Variable in class org.anchoranalysis.spatial.point.Tuple3d
z - Variable in class org.anchoranalysis.spatial.point.Tuple3f
z - Variable in class org.anchoranalysis.spatial.point.Tuple3i
z() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
z() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
z() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
z() - Method in class org.anchoranalysis.spatial.Extent
z() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
z() - Method in class org.anchoranalysis.spatial.point.Tuple3d
z() - Method in class org.anchoranalysis.spatial.point.Tuple3f
z() - Method in class org.anchoranalysis.spatial.point.Tuple3i
z(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
z(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains: Is this value in the z-dimension within the bounding box range?
Z - org.anchoranalysis.spatial.axis.AxisType
Z_ONLY - org.anchoranalysis.image.voxel.object.morphological.SelectDimensions: The dilation applies only in the Z-dimension.
zChange - Variable in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
ZeroOutsideMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.
ZeroOutsideMask() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.ZeroOutsideMask
zeroValue(int) - Method in class org.anchoranalysis.math.histogram.Histogram
zFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
zRelative() - Method in class org.anchoranalysis.image.core.dimensions.Resolution: Assumes x and y has constant resolution, and gives the relative resolution of z to x or y.
zScore(double) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
ZScore<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.score
ZScore() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.score.ZScore

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